Paul McGuinness' side finished the game with 10 men when Tyler Blackett was sent off for dissent late on and Sam Johnstone had to be at his best to preserve a clean sheet.
Will Keane has been in good form since regaining full fitness - scoring a hat-trick in the FA Youth Cup semi-final second leg against Chelsea, coming closest to breaking the deadlock for the reserves on Thursday and now netting the crucial strike in this success.
United could have been ahead as early as the second minute as Jesse Lingard hit a post and Mats Daehli spurned a golden chance to open his Under-18 account from the rebound by firing over an open goal.
The strong wind and bobbly pitch didn't help matters but there was a chance apiece just before the break with Will Keane pouncing on a poor defensive header to lob just wide and Johnstone being forced into a smart stop at the other end.
The match hinged on a period of play a few minutes into the second half. Sam Patterson's cross-cum-shot hit the bar and United went straight up the other end to score with Will Keane latching onto a loose ball on the edge of the box and finishing through the goalkeeper's legs with his left foot.
Lingard shot wide and substitute Rafael Leao had a drive tipped over as the FA Youth Cup finalists looked to seal victory, with Michael Keane moving into midfield following the introduction of Tom Thorpe.
Johnstone had to pull off a brilliant double save to deny Erico Sousa when an equaliser seemed