Substitute Rooney sent a powerful header over American goalkeeper Brad Friedel in the 74th minute to settle the first meeting of U.S.-owned clubs in an English final.
"I had a little bit of a sore knee for a couple of weeks and I felt it in the game" Rooney said. "I'm delighted to score the winning goal in a Wembley final for the first time."
James Milner had put Villa ahead from the penalty spot after five minutes, but Michael Owen quickly tied it for the English champions.
Prevailing in the 50th League Cup final provided Alex Ferguson with his 26th title since joining United in 1986.
Yet a sign of where England's second-tier knockout competition fits on Ferguson's priority list — behind the Champions League and Premier League — was evident in Owen being selected to lead the attack from the start over the in-form Rooney.
And Ferguson's plans seemed to be unraveling when Gabriel Agbonlahor latched onto Ashley Young's long ball only to be hauled down by Nemanja Vidic.
Despite not even booking the Serbian for denying a goal-scoring opportunity, referee Phil Dowd pointed to the penalty spot and Milner slotted the ball into the bottom right corner, sending Tomasz Kuszczak the wrong way.
"We started really well," Friedel said. "Perhaps it's unfortunate we weren't up a man from the start."
With Rooney on the bench, Owen had a rare platform to convince Ferguson to use him more regularly and, perhaps one last chance, to prompt England coach Fabio Capello to include him in his World Cup squad.
The 30-year-old Owen scored 12 minutes into his first Wembley final. Dimitar Berbatov stole the ball off Richard Dunne, and while the Villa center back caught up with the advancing Bulgaria forward, his tackle pushed the ball toward Owen, who struck the ball beyond Brad Friedel.
It was Owen's last significant contribution to the final. As has been the story of his recent career, Owen was forced off with a hamstring injury in the 42nd — another sign for both Ferguson and Capello of the forward's ongoing fitness struggles.
"I didn't think of who was watching. It was a real chance for me because I haven't started too many games," Owen said. "I just want to play for Man United and if that gets me recognition, then great. I've been to many World Cups and European Championships. If I don't go, it gives someone else a chance."
Owen's departure gave Rooney an opportunity to continue his hot goal-scoring streak.
After good buildup play between Berbatov and Antonio Valencia, Rooney met Valencia's cross from close range with a header that had too much power and accuracy for Friedel to stop.
"I knew he would enter the fray at some stage," Ferguson said of Rooney. "He's a world class player and arguably among top three players in the world. He made it more exciting."
Rooney was only denied his 29th goal of the season by the post minutes later.
Dowd's inconsistent refereeing in the first half irritated Villa manager Martin O'Neill. While Vidic escaped a third-minute sending off and Michael Carrick avoided a yellow card for a challenge on Emile Heskey, Villa's James Collins was booked for bringing down Owen as was Stewart Downing for a late challenge on Patrice Evra.
Evra was, however, booked just before the break for a lunging challenge on Ashley Young.
Villa, which is through to the FA Cup quarterfinals, could potentially return to Wembley in the final in May and end its 14-year wait for a trophy.