Andras Stieber powered home a superb volley as Villa U21s bagged three points in their first league game of 2014.
Stieber struck with an unstoppable effort on the hour mark to settle a hard-fought contest at Goodison Park.
Villa created a host of clear-cut opportunities but also had to rely on goalkeeper Brad Watkins, who made a string of important saves.
Gordon Cowans' team made a bright start with Jerell Sellars firing just wide from 20 yards after expertly controlling a high ball.
Skipper Daniel Johnson also curled an shot just off target, while a Callum Robinson header was tipped around the post by Everton keeper Russell Griffiths.
And, towards the end of the half, Johnson played a delightful one-two with Sellars but couldn't keep his effort down.
The Toffees had chances too, with Watkins making a couple of crucial early saves.
The Villa keeper parried Calum Dyson's fierce low drive, as well as keeping out a first-time volley from Joe Williams.
Gethin Jones had two opportunities in quick succession but one was blocked by Watkins and the other went wide.
However, the first half was marred by an injury to Villa full-back Liam Bateman, who was stretchered off after 21 minutes with a suspected broken leg.
Early in the second half, Graham Burke attempted a cheeky overhead kick from six-yards before curling an effort just wide from the edge of the box.
The away side's deadlock-breaker was well worth the wait.
Daniel O'Brien's cross from the right was cleared into the path of Stieber who unleashed a terrific 20-yard volley which nestled in the corner of the net.
The Toffees had a couple of great chances to equalise through Williams who sidefooted wide from close range and substitute Harry Charsley who headed against the post.
Callum Robinson nearly put the game to bed when Griffiths scooped away his low drive but Villa did enough to bag the points.
EVERTON: Griffiths, McLaughlin, Touray, Ledson, Kenny, Langton, Green, Williams, C Duffus, Dyson, Jones. Subs: Hewelt, Charsley [for Jones, 69], T Duffus, Connolly [for Green, 82], Dowell [for Dyson, 57].
VILLA: Watkins, Webb, Kinsella, Bateman, Donacien, Lewis, Stieber, Sellars, Robinson, Johnson (c), Burke. Subs: O'Brien [for Bateman, 21], Grant, T Strain, Zazrivec, McKirdy.