The result meant little in terms of the Red Devils' position on the standings, with the English giants already guaranteed to finish the campaign in sixth place, while Southampton remain on track for a top-half finish.
The Saints were handed the chance to take a fifth-minute lead as Eric Bailly used his arm to control in the area to give away a penalty, although Manolo Gabbiadini lacked conviction from the spot and Sergio Romero guessed right to make the save.
Bailly almost made immediate amends with a rare shot at the other end of the pitch which forced Fraser Forster into making a save.
Anthony Martial probably should have done better after being played in by Wayne Rooney following some deft control from the Englishman, although his forward partner failed to get the right connection on his shot and dragged miserably wide.
The Red Devils had a great chance to break the deadlock midway through the second-half as Chris Smalling stormed down the channel before crossing in for Rooney, who in turn laid the ball off for Juan Mata, although the Spaniard blasted his shot way over, much to the dismay of manager Jose Mourinho.
The Saints almost snatched it in the final eight minutes as Jay Rodriguez managed to get in behind the United defence, although the forward almost expected an offside flag that never came and in his confusion fired a weak shot wide of the mark.