The youngsters slipped to their first defeat in four matches in the Under-18s Barclays Premier League on Saturday morning.
Hosts Manchester United ran into a two goal lead during the first half at Carrington thanks to a brace of strikes from Ashley Fletcher.
United’s in-form striker grabbed his sixth and seventh goals of the campaign, with the first arriving from a follow up inside the area on 26 minutes after Saints stopper Harry Isted had parried the ball from a cross.
Fletcher notched his second just over ten minutes later by applying a close range finish to a cross.
Saints rallied in the second period and clawed a goal back in the 67th minute when full back Tom Leggett crossed for substitute Marcus BARNES who turned and struck a sweet, low shot into the back of the net to give Saints hope of a comeback.
From then on, the visitors did look the more likely to score, and perhaps should have done too, with Sam Gallagher going close on a handful of occasions, but the striker was unable to make the most of the chances that came his way.
Although not content with their slender advantage, the hosts were restricted for much of the second 45 by the resolute Saints backline, who were unfortunate not to have more to show for their efforts by the end of the game.
U18s coach Jason Dodd said: “It was a game of two halves. In the first half we didn’t do what we’ve been working at and although we did actually have a few chances, we didn’t make the most of them.
“There wasn’t much in it and we had a little chat with the lads at half-time because they weren’t all doing what we’d asked them to do.
“We made more chances in the second half and we’ve come off the pitch with people saying that we were the best team to have played them this season, which is pleasing.
“Although we should have scored again, there are a lot of positives to take away from the game.
“Performance-wise I thought Tom Leggett was exceptional and led by example, and there were more good performers in the second half.
“We know where we are as a squad, we’re still a young side, and we’ll continue to give everyone an opportunity in the games ahead.”
Southampton Under-18s: Harry Isted, Tom Leggett, Kyle Clinton, Josh Debayo, Isaac Nehemie, Dan Demkiv (Marcus Barnes 60), Charlie Higgins (Armani Little 70), Niall Mason, Jake Hesketh, Josh Sims (Harley Willard 70), Sam Gallagher.