Under-strength they might have been, but Everton were a goal up with four minutes after a bright start which saw Villa concede two corners.
The first Mikel Arteta kick just skimmed off the head of Joleon Lescott, but the second found the head of Tim Cahill who looked to have buried it past Brad Friedel.
The Aussie however had not banked on Stiliyan Petrov clearing off the line. It was only a temporary reprieve though as Petrov's handled clearance fell to Jack Rodwell, who slammed the ball in the net from five yards.
In the eighth minute though Villa levelled through a James Milner penalty after Tony Hibbert had brought down Gabriel Agbonlahor inches inside Tim Howard's penalty area.
Though the US keeper got down to touch James Milner's spot-kick, but it somehow squirmed under his body to level the scores and ensure the tie had the makings of a cup classic.
Everton, rather than letting their heads drop, kept pressing forward with Cahill and Victor Anichebe in particular giving the Villa back four a torrid time.
Everton got their own penalty in 23 minutes when Steve Sidwell brought Anichebe down in the area after a sparkling run deep into Villa territory saw him evade the challenges of several defenders.
Arteta strode forward to send Friedel the wrong way and Everton were back in the lead.
The visitors began to change tack as Friedal started launching long balls up to John Carew's head, a tactic that was beginning to pay dividends in the last 15 minutes of the half by unsettling the Everton backline.
Agbonlahor should have levelled when a pin-point Ashley Young cross hit him on the shoulder, when a header from six yards would have done the job.
Everton started the second half as they started the first, pushing, prodding and probing Villa's defence as the Toffees went looking for the goal that would seal their passage to the last eight.
Villa were still capable of rattling the Blues back four though, one incident saw Phil Neville having to clear for a corner as the ball pinged around the area evading both Phil Jagielka and Lescott.
An inspired piece of keeping from Howard kept the home side ahead in the 60th minute as a Milner cross found the foot of Carew, whose shot from eight yards out looked to be heading for the bottom corner until the American keeper launched himself across his goal and tipped it round the post.
Villa were looking the fresher as the game entered the last 20 minutes as Everton failed to close men down as effectively as they had all game and the visitors threatened an equaliser on a couple of occasions.
Everton effectively secured victory with in the 75th minute as Cahill started and finished a move that ended with the ball nestling in the back of Friedel's net.
The Aussie passed to Anichebe who crossed the ball towards a waiting Dan Gosling in the Villa area, however the youngster slipped as the ball sailed past him.
Cahill had continued his initial run into the area and fired in at the back post to give his side a crucial two-goal cushion.