An Everton side determined to break a two-game losing streak came out all guns blazing as Lee Carsley blasted a shot at the Villa goal which Peter Enckelman did well to handle.
The Merseysiders chased down every ball as they remained the hungrier team throughout the match. An excellent though ball from David Unsworth left Rooney with a one on one with Enckelman, but as the Goodison faithful cheered in anticipation the teenager's dragged his shot wide of the left post.
Moments after a deft lob from Rooney cleared the villa defence to leave Steve Watson through on goal but his volley sailed straight into the stands.
Villa managed to quell a flurry of well constructed attacks from Everton as the game became physical.
The deadlock was finally broken when a lax clearance from the Everton defence gave Villa their first real chance of the game and Marcus Allback gave the Midlanders the lead as he calmly stroked the ball past Richard Wright in the 48th minute.
Duncan Ferguson made an appearance in the 54th minute when he came on for Unsworth as David Moyes tried to inject some life into a deflated Everton side.
The move paid dividends minute later as the Scot was involved in the build-up of play which resulted in the Blues equaliser.
Gary Naysmith whipped in a cross which was met by a powerful header from Kevin Campbell in the 58th minute.
Ferguson was a dominant force on his return to the first team making a sequence of fine passes and solid tackles. He was only kept off the scoresheet by a few heroic saves by the Villa keeper.
The match seemed to have become a stalemate but the Goodison Park faithful erupted in the 89th minute as wonderkid Rooney thundered a low drive past the bewildered Enckelman to earn Everton three points to keep their European hopes alive.