After the game, José Mourinho bemoaned what he perceived to be a refereeing error, with Maya Yoshida's handling of the ball in the first half deemed unintentional, yet the home side were sluggish and impotent in attack.
The result means United end 2017 in third place in the Premier League, leapfrogged by Chelsea and trailing Manchester City by 14 points (17 if Pep Guardiola's side win their game in hand against Crystal Palace on New Years' Eve).
Here are the five things we learned from the Old Trafford stalemate.
Mkhitaryan flops again
Armenian creator Henrikh Mkhitaryan was handed his first start in almost two months, having been jettisoned from the staring line-up following string of sub-par displays.
The former Borussia Dortmund star, however, failed to grasp the opportunity he was given, putting in the kind of performance that will only add further fuel to rumours of a potential January exit.
Starting on the left side of the United attack, a somewhat unfamiliar position or the 28-year-old, Mkhitaryan was wasteful, swinging wild crosses beyond his onrushing team-mates, and generally sloppy in possession, visibly lacking confidence.
Mkhitaryan was credited with tree key passes, but too often United's attacks broke down at his feet, with television cameras capturing Mourinho looking indignant on the bench after one particularly errant cross in the first half.
United blunt in attack
The Red Devils enjoyed a 54.6 per cent share of possession, playing much of the game in the Saints' half, but United struggled to truly threaten goal throughout.
A head injury ended Romelu Lukaku's evening around the ten-minute mark, thus inevitably taking away some of the home side's potency. But even accounting for the powerful Belgian's exit, United were stagnant and lacking creatively.
United only hit the target three times against the Saints – the same number of shots on goal as Southampton. Indeed, neither goalkeeper was troubled after the 58th minute, despite Mourinho's men in desperate need of three points.
There were times last season when United were frustrated at Old Trafford after banging on the door for 90 minutes, denied by a combination of fine defending and pure bad luck.
That wasn't the case here; this United performance was a throwback to the days of Louis van Gaal's possession-for-possession's-sake brand of uninspiring football.
Van Dijk who?
There was one notable absentee for Southampton at Old Trafford – in addition to benched goalkeeper Fraser Forster: Virgil van Dijk. The totemic Dutch centre-back will become the most expensive defender in history on January 1, when he will officially becomes a Liverpool player in a £75million deal.
Without the former Celtic man, who has admittedly been out of form this term, the Saints' central defensive duo of Maya Yoshida and man of the match Wesley Hoedt were outstanding, constantly denying United space in and around the penalty area and dominating their individual duels.
Hoedt made a game-leading ten clearances, while Yoshida won more headers (four) than any other player on the pitch.
Time for a change of shape for United?
Some of United's issues appear to stem from their formation. Despite dalliances with 3-5-2 earlier in the campaign, Mourinho has reverted to his favoured 4-2-3-1 shape of late, but it doesn't seem to optimise the gifts of his best players.
Playing alongside Nemanja Matić in a double pivot, Paul Pogba's starting position is too deep for him to consistently affect the game in advanced positions, where he is most comfortable and dangerous to the opopostion.
And out wide, Mourinho tends to start with inverted wingers, players who look to come inside on to their stronger foot – against Southampton, it was the left-footed Juan Mata on the right and right-footed Mkhitaryan on the left.
In 4-2-3-1, the presence of a No.10 – Jesse Lingard here – and said player's marker(s) means the wide men's path inside is congested. A 4-3-3 system, for example, would have no such issues, while also offering Pogba more offensive freedom as part of a midfield three.
Treatment of head injuries improving
A clash of heads with Hoedt left Lukaku in a heap on the turf with less than ten minutes played. While no one will have enjoyed seeing the former Everton man alarmingly prostrate and stretchered off the pitch, the immediate and considered medical attention he received was encouraging.
As head injuries become more of a talking point within sport, more focus is trained of their prevention and treatment, with the true dangers of concussions only recently coming to light.
There are now protocols in place for such situations, regulations that prevent a concussed player from returning to action within a defined period, and the treatment Lukaku received in the aftermath of his own cranial blow was commendable.
Mourinho won't be happy with the prospect of losing his star striker for any period of time, but even he would have to agree that the advancements in how such injuries are handled is good for the sport and the long-term health of its stars; the days of playing on after having you ‘bell rung' are, thankfully, in the past.