A first-half brace from Callum Robinson and a late Graham Burke strike helped Villa get back to winning ways in the Barclays U21 Premier League.
Gordon Cowans' team got off to a brilliant start at the Weaver Stadium with Robinson scoring twice inside the opening 12 minutes.
Stoke hit back through Derice Richards but Graham Burke scored in the final minute to seal the victory.
A quickfire double from Robinson gave Villa the perfect start.
In the fifth minute, he was quick to punish goalkeeper Daniel Bachmann who miscontrolled a backpass from former Villa academy player Mason Watkins-Clark.
After robbing Bachmann of possession, Robinson was left with a simple finish into an empty net.
Seven minutes later, the teenage hotshot cut inside from the byline and fired a left-foot shot into the bottom corner to make it 2-0.
Watkins-Clark made a last-ditch interception to deny Robinson a third moments later.
Stoke pulled a goal back on 19 minutes through Derice Richards, who lashed a shot high into the net after Villa struggled to deal with a cross into the six-yard box.
Graham Burke went close for the visitors just before the break but Bachmann used his feet to thwart the Irishman.
Ben Heneghan had the chance to equalise early in the second period but headed wide from Eddy Lecygne's corner.
Substitute David Moli also struck a fierce volley which Villa keeper Brad Watkins took two attempts to get under control.
Robinson had two great opportunities to complete his hat-trick but was just off target on both occasions.
The first one saw him steer an effort inches wide across goal after outmuscling Watkins-Clark.
He then cut in from the left and struck a powerful drive just past the far post.
But Burke sealed the victory in the last minute, superbly firing home a low half-volley from the edge of the box.
STOKE: Bachmann, Wheeler, Gomez, Ward, Heneghan, Watkins-Clark, Cook, Lecygne, Skapetis, Richards, Taylor. Subs: Moli [for Cook HT], Eve, Sanders, Monlouis [for Taylor 63], O'Reilly [for Heneghan 72].
VILLA: Watkins, Webb, Wildin, Stieber, Donacien, Lewis, R Strain, Burke, Robinson, Johnson, Graham. Subs: O'Brien, Hill, T Strain, Sellars [for R Strain HT], McKirdy.