The doubts have been there all season where the defence is concerned - "Cartoon Cavalcade" is how Alex Ferguson described it last month - and with its occupants so obviously covering for a David de Gea who is clamped to his six-yard box when the high ball comes in, it does not take a stroke of tactical genius to sense an exploitable weakness.
It mattered most that United - with Rooney back at his sharpest - won while not playing well. But where the looming prospect of Jose Mourinho's Real Madrid are concerned, it mattered also that Rio Ferdinand was required from the bench from the hour mark, with Nemanja Vidic quite unconvincing - and Chris Smalling especially so. It will be a comfort to many that the word from Ferdinand's camp yesterday was that the absence of a new contract is no cause for concern and that it will come in time.
Ferguson blamed the pitch for the way United allowed Southampton back into the game. "We tried to play the way we normally play but found it difficult because the pitch had dried out a lot. It required us to play the ball in the gaps, which we don't normally do."
But it would be too convenient to remove Southampton and Mauricio Pochettino's pressing game from the story. United's midfield was simply not physical enough to handle it.
Pochettino, whose tactical confidence and excellent post-match conversation with the press was encouraging, said that "We saw we had a chance to press up there and destroy their creativity - especially cancelling out the channels (and) the passes into Rooney, (Danny) Welbeck or (Robin) Van Persie."
It certainly worked. Southampton controlled United for much of a second period which had Ferguson exhorting his men to bypass midfield. "Southampton won a lot of 50-50s as our players looked to take a touch," he admitted. "In the second half they put in the best performance anyone has put in here this season."
It was an impressive turnaround because the procession towards victory had the strong but fatalistic Southampton contingent ironically chanting "We're going to win 3-2" before half-time.
Their pitifully brief hope was delivered by the goalkeeper who keeps raising questions about himself.
It was a dreadful backpass that Michael Carrick levered towards De Gea after 129 seconds of the game had elapsed, giving Jay Rodriguez the chance to race in and challenge for it. But De Gea's reaction was a flinching, mincing one.
You expect a United goalkeeper to place himself between striker and goal, rather than place a weak tackle which Rodriquez won and advanced to place the ball into the net.
Pochettino later suggested, on the topic of De Gea, that goalkeepers from the Spanish league - where he managed and played Espanyol - find the Premier League's physicality hard-going. De Gea's second-half fumble of Rickie Lambert's dipping free-kick, before snatching the ball up from the advancing substitute Adam Lallana, only perpetuated the sense of a goalkeeper living on his nerves.
United, who had already fallen behind 11 times in the Premier League this season and had won eight of those fixtures, equalised inside five minutes.
Shinji Kagawa took hold of a sliced Southampton ball in midfield and measured out a pass through the central channel that Rooney clipped in. Kagawa had hit the post before Rooney took United ahead.
Van Persie's free-kick over the penalty area was headed athletically back into Rooney's path by Patrice Evra and the striker moved beyond the Best record.
United thought they were home when Rooney's arced ball found Van Persie's head and he was unlucky to be judged fractionally offside, on 75 minutes.
The stadium was emptying well before the end though Ferguson, pacing his technical zone for much of the second period, will have read the signs.
He knows his side are not an indomitable force as they approach the months which bring a season's triumphs and disasters.