Rooney was named among the substitutes despite his recent red-hot form, with United boss Sir Alex Ferguson opting for a Michael Owen and Dimitar Berbatov frontline.
Ferguson was rewarded with telling contributions from both Owen and Rooney as the former fired the Red Devils back on level terms before limping out of his first Wembley final in the 42nd minute with a hamstring injury.
United were much changed from their midweek Premier League victory over West Ham as Owen, Tomasz Kuszczak, Rafael, Johnny Evans, Darren Fletcher, Michael Carrick and Ji-Sung Park all came into the starting line-up.
Villa boss Martin O'Neill was able to recall the fit-again Stiliyan Petrov and Brad Friedel, James Collins and Emile Heskey to his side and the Midlands club drew first blood with just five minutes on the clock.
Nemanja Vidic pulled down the speedy Gabriel Agbonlahor in the box and referee Phil Dowd had no hesitation in awarding a penalty.
Villa were furious that Dowd did not send off Vidic as the Serbia defender was clearly the last man, but their irritation turned to joy when James Milner slammed home a low spot-kick to Kuszczak's left.
But United, with their full complement of players, were not behind for long as a lively Owen found himself in the right place at the right time just seven minutes later.
Berbatov won possession and headed for the penalty area where the recovering Richard Dunne managed to nudge the ball clear of his control.
However, it fell perfectly for Owen to find the back of the net with a trademark angled shot.
Milner forced Kuszczak to parry away his stinging 25-yard drive, while Park's close-range shot off the post came close to edging United in front as an entertaining first period drew to a close with the arrival of Rooney.
Carrick tested Friedel with a powerful drive as United began to dominate possession and restrict Villa to rare forays into their half with swift breaks.
But Friedel was beaten 16 minutes from time when Rooney took his season's tally to 28 goals in all competitions with a looping header.
Antonio Valencia floated over a cross and the in-form striker guided an angled header over the outstretched hand of Friedel and into the back of the net.
Rooney headed another Valencia cross against the base of the upright moments later as he was denied what would have been a game-clinching second goal of the afternoon.
At the other end, Emile Heskey's own deflected header off Vidic's shoulder landed on top of the crossbar in the closest they would come to restoring parity as United played out time to win the Carling Cup for the second successive season.