Marco Silva's side led 2-1 with 19 minutes remaining but a brace from substitute Michy Batshuayi either side of Cèsar Azpilicueta's late winner turned a dramatic game on its head and handed the Blues a three much-needed points.
Pedro put the champions in front with a superb first-time curling effort which clipped in off the post. But Watford refused to give up and equalised when Abdoulaye Doucouré thrashed home from José Holebas' long throw in first-half stoppage time.
Watford started the second period on the front foot and Richarlison, in particular, squandered several fine chances to put the visitors out of sight.
Roberto Pereyra did give the Hornets the lead four minutes into the second half, latching onto Richarlison's pass and slotting home. And Watford went in search of more.
But they were made to pay for their profligacy as Chelsea first equalised through Batshuayi and then won it at the death thanks to Azpilicueta's header. Batshuayi then capitalised to add a fourth in stoppage time.
Thibaut Courtois – 6
The Belgian stopper, making his 100th Premier League appearance for Chelsea, had to be alert throughout with Watford piling on the pressure in the second half.
He did well to push Tom Cleverley's firmly-struck free-kick to safety after half an hour but there was nothing he could do about either of the goals.
Antonio Rüdiger – 7
Dropped for the 2-1 loss at Crystal Palace a week ago, the German international was reinstated to the side, allowing Azpilicueta to move forward and play at right wing-back.
He might have expected, therefore, more assistance from the Spanish international when it came to dealing with the liveware that was Richarlison who caused the Confederations Cup winner problems time and time again.
But the former Roma man came out on top, winning both the tackles he attempted and 88 per cent of his aerial duels.
David Luiz – 7
Back in defence after a midweek foray into midfield for the Champions League draw with Roma, Luiz would have known what awaited him after Watford skipper Troy Deeney's well-publicised comments about roughing up Arsenal‘s backline a week ago.
But the former Paris Saint-Germain and Benfica man is clearly made of sterner stuff than Per Mertesacker and co. and came out on top in the physical duel with Watford's No.9, winning four of five aerial duels and succeeding with 67 per cent of his tackles.
It's no secret the Blues skipper is woefully short of form and given the pace and directness of Watford wing-back Kiko Femenía it was perhaps something of a surprise to see Andreas Christensen left out given his mobility.
Cahill endured a tough game with the Spaniard happy to run at him throughout. On another afternoon it could have proved fatal for the Blues. Long-term questions of Cahill's suitability in one of the wide positions in a back three are becoming louder.
César Azpilicueta – 7.5
In the early exchanges it was Chelsea's Swiss Army knife of a defender who caused the visitors the most problems. The Spaniard was pushed forward to play right wing-back but you would never have known it wasn't his natural position as he galloped forward time and time again.
Azpilicueta caused José Holebas and Britos problems down Watford's left and his delivery was every bit as impressive on a few occasions. But his effectiveness waned in the second period. That was until the former Marseille man popped up unmarked to nod home the winner at the death.
Cesc Fàbregas – 6.5
Should really have taken the game away from Watford a matter of minutes after Pedro opened the scoring for Conte's men. But when the ball somehow found him in acres of space Fàbregas over complicated matters by attempting to chip Heurelho Gomes and was left with egg on his face.
He did rather better with his next chance, though, letting fly from outside the penalty area only to find Gomes in the way once again.
Tiémoué Bakayoko – 6
Clearly still short of fitness after picking up an injury in the week, the former Monaco man struggled to really get control on things despite winning all five of his tackles.
He was never able to get to grips with Doucouré in the engine room and it was the Watford man who came out on top in the battle of the rangy French midfielders.
Marcos Alonso – 5
An underrated and under appreciated attacking outlet for the Blues, Alonso was unable to stretch Watford down their right and did not complete a dribble in the game before being hooked.
Pedro – 7
The former Barcelona forward endured a slow start to life at Chelsea. But now in his third season, Pedro's importance to the Blues is absolute.
At a time when there were a few nerves around Stamford Bridge following a winless run of three games, it was the Spanish international who calmed things down by whipping home a sumptuous opener from outside the box.
That was his 18th Premier League goal for the Blues and means he has now been involved in 30 in just 55 starts in the league.
Equally impressive is the fact he has had a hand in more goals in 2017 than any other Chelsea player, registering 12 goals and eight assists.
Chelsea's star man in an attacking sense last season, it has not happened yet for the former Real Madrid transfer target this term.
In fairness to Hazard he is still recovering from the ankle fracture which appeared to scupper any chance of a move to the Bernabéu and he was unable to stamp his usual influence on this encounter.
Scarcely able to escape the attentions of Watford centre-back Christian Kabasele, the Spaniard cut a frustrated and lonely figure up front. And his frustration boiled over in the second half when he was booked for needlessly shoving the Belgian near the halfway line.
He was substituted shortly after having made little to no impact in his hour on the field.
Michy Batshuayi (for Álvaro Morata) – 8: Replaced the Spaniard after an hour having scored home and away against the Hornets last season. And he repeated the trick, escaping the attentions of Kabasele to nod home Pedro's right-wing cross for the equaliser before outmuscling the Belgian to bag Chelsea's fourth.
Willian (for Marcos Alonso) – 7: On for the ineffectual Alonso after 68 minutes, the Brazilian's arrival prompted a change in shape for Chelsea and he supplied the cross for Azpilicueta's winner.
Davide Zappacosta (for Pedro) – N/A: Despite getting just a handful of minutes he nearly supplied a winner for Batshuayi moments before Azpilucueta did head home the clincher.
Heurelho Gomes – 6.5
There was nothing the Hornets' No.1 could do about any of Chelsea's goals, not least Pedro's stunning opener which clipped the post on its way in.
He did well to limit the damage a few minutes later when the ball reaches Cesc Fàbregas in acres of space, getting a hand up to block the midfielder's deft chip.
Adrian Mariappa – 6.5
Making his 100th Premier League appearance on the right-hand side of the Hornets' back three, Mariappa looked comfortable and was even able to get forward in support in the first half.
He almost gifted Chelsea the lead seconds after the restart when he stretched to poke a cross from the right over his own crossbar but that was a rare blip in an otherwise solid display which saw him shackle Marcos Alonso down the left.
Playing at the heart of Watford's back three, the Belgian did an impressive job of shackling Chelsea's top scorer Morata and the Spaniard was withdrawn after an hour having failed to get any chance out the former Genk man.
However, that all changed when substitute Batshuayi was introduced. It was the Belgian who darted across him to nod home the Blues' leveller and he was outmuscled for the fourth.
Miguel Britos – 6
Culpable on Chelsea's fourth thanks to a ludicrous attempted chip which was charged down enabling Batshuayi to score, that error marred an otherwise solid display.
There were times in the first half where the Uruguayan was unsettled by Azpilicueta but he got the upper hand and worked well in tandem with left wing-back Holebas.
Kiko Femenía – 6.5
A winger until last season, Femenía showed his tendencies to bomb forward throughout. Another day he would have had an assist to his name, too, but Richarlison somehow failed to convert his delightful ball to the back post early in the second period.
On the defensive side the former Alavés man did well to neutralise the threat of Chelsea's left wing-back Alonso who was a peripheral figure in attack for the hosts.
However, it was Femenía who completely lost countryman Azpilicueta at the crucial moment, allowing him to get goal side and nod in the winner.
Tom Cleverley – 6.5
The former Manchester United midfielder has been talked about for a possible England recall, so impressive has his form been in the early weeks of the season.
It is, therefore, imperative the 27-year-old takes the chance to underline his quality in games such as this. But he was unable to do so, winning just one of the four tackles he attempted and being dribbled past three times.
Cleverley had a chance with a free-kick after half an hour which brought a good stop out of Thibaut Courtois.
How long until bigger clubs start to sniff around the French powerhouse? Doucouré was persona non grata at Vicarage Road at the start of last season and only remained at the club as the Hornets were unable to find a club prepared to take him on loan.
In the second half of the season he flourished, though, and he has become the heartbeat of Watford's side this season.
At Stamford Bridge he was the pick of the visitors' midfield, using his positional awareness to recover the ball and keeping things moving with quick and accurate passes, connecting with 97 per cent – more than any other starter.
And he capped a fine performance by anticipating a dropping ball from Holebas' long throw to lash a rasping effort past Courtois at his near post and equalise for the visitors just before half time.
Doucouré is going to the top echelons of the Premier League. With or without Watford.
The Greek international initially struggled against Azpilicueta who was allowed far too much space and time down the right-hand side to swing in several dangerous deliveries.
But Holebas gradually got the grips with the Chelsea wing-back and was always quick to get forward in support of Richarlison ahead of him.
Roberto Pereyra – 7
Deployed on the right-hand side of a front three for the second game in a row, the Argentine playmaker was at the centre of everything good for the Hornets in the early stages.
Drifting wide to hug the touchline at times before coming back inside, Pereyra linked well with Deeney and looked the player most likely to unpick Chelsea's defence in the first half.
In the second period he made good on that promise, starting and finishing the move for Watford's second with a well-taken goal.
Troy Deeney – 6.5
After his controversial comments about Arsenal‘s lack of cojones a week ago it was a rather quieter afternoon's work for the Watford skipper who was restored to the starting XI in preference to Andre Gray.
He still put himself about and tried to use his physique to unsettle the Blues' backline but it did not have the desired effect and he was well marshalled by David Luiz.
Withdrawn ten minutes from the end to allow Silva to put another body in midfield in the shape of Ben Watson, a decision which contributed the turnaround.
Richarlison – 7.5
Reportedly a Chelsea transfer target in the summer, the 20-year-old forward has been one of the stars of Watford's season following his £11.2million switch from Fluminense and was again the Hornets' star man.
He should have added to the three goals he's already scored this season early in the second half when he failed to convert Femenía's inch-perfect cross to the back post.
However, Richarlison atoned for that glaring miss by providing the assist for Pereyra's all-important goal. Whether intentional or otherwise, it was his pass which found the former Juventus men to stroke beyond Courtois.
The duel between Richarlison Antonio Rüdiger was a feature throughout and the Brazilian got the better of the Blues centre-half on multiple occasions, not least when the former Roma defender was booked midway through the first half.
André Carrillo (for Roberto Pereyra) – 6: Introduced in place of goalscorer Pereyra after 65 minutes. He was immediately into the action, providing a dangerous low cross for Deeney which was just snuffed out by Luiz.
Ben Watson (for Troy Deeney) – N/A: Introduced to shore things up ten minutes from the end. But it did not work out that way.
Andre Gray (for Adrian Mariappa) – N/A: Chucked on as a late, desperate measure to find an equaliser.