Villa missed out on the chance to go top of their Barclays U21 Premier League group after being overpowered by an experienced Manchester United outfit.
Bebe and Federico Macheda were on target for the Red Devils, who produced a storming second-half display to leapfrog Villa into second place in Group 2.
It means the Young Lions must now beat leaders Tottenham Hotspur at Villa Park next week to clinch top spot.
With Wednesday's FA Youth Cup clash in mind, Villa made four changes from the 3-2 win over Newcastle eight days ago.
Calum Barrett returned in goal while Daniel Devine, Mason Watkins-Clark and Brad Lewis also came into the line-up.
Craig Hill, Liam Bateman, Josh Webb and Jordan Graham - all likely candidates for Youth Cup selection - were left out.
The boys in claret and blue faced a stern test against a strong Man United side featuring summer signings Nick Powell and Alexander Buttner as well as long-time nemesis Macheda.
A defeat for Group 2 leaders Tottenham at Sunderland earlier in the day meant Villa could move into top spot with a victory.
This added incentive seemed to spur the hosts on in the early stages.
They made a rapid start and Daniel Johnson dragged a shot just wide of the target in the second minute after a neat passing move from Graham Burke and Andras Stieber on the left hand side.
Moments later Stieber should have done better after being picked out by Burke.
The Irish forward surged past defender Tom Thorpe and slotted left to Stieber but the winger opted to cross rather than shoot.
Then Burke called goalkeeper Jonathan Sutherland into action with a low shot from a tight angle which was pushed to safety.
United, though, moved through the gears towards the end of the half.
Macheda met a cross from Ryan Tunnicliffe at the near post but his volley was deflected wide and, from the resulting corner, Thorpe headed off target.
But the away side really took charge after the restart.
Seven minutes into the second-half, Bebe surged through the middle of the park and hit a thumping left-foot drive past Calum Barrett to give United the lead.
He nearly had a second six minutes later but Barrett got down well to keep out his low shot which seemed destined for the bottom corner.
Barrett then stood tall to deny Powell in a one-on-one situation, before Larnell Cole was guilty of a glaring close range miss.
The United wideman struck the post after receiving Macheda's lay-off, although the Italian perhaps should have taken on the shot himself.
Villa rarely threatened in the second period although Michael Drennan miscued an overhead kick late on from substitute Callum Robinson's cross.
Macheda wrapped things up in the 89th minute with a low shot from the edge of the box which crept under Barrett.
VILLA: Barrett, Watkins-Clark, Devine, Donacien, Lewis, Barton, Johnson, Carruthers, Stieber, Burke, Drennan. Subs: Robinson [for Watkins-Clark, 60], Watkins, O'Brien, Sellars, Cowans.
MAN UTD: Sutherland, Vermijl, Buttner, Thorpe, Wootton, Tunnicliffe, Bebe, Powell, Macheda, Petrucci, Cole. Subs: McGinty [for Buttner, HT], Gollini, Veseli [for Powell, 90], Lawrence, Fornasier [for Bebe, 84].