The in-form England striker was rested by boss Sir Alex Ferguson but entered the fray just before half-time after Michael Owen had limped off with a hamstring strain.
And he soon stole the plaudits with a superb 74th header from Antonio Valencia’s cross for his 28th goal of an explosive season.
But Rooney’s cameo role was soured by the recurrence of a knock to his right knee, which Ferguson hinted could prevent him from playing in England’s friendly with Egypt on Wednesday night.
Owen earlier hauled United level after James Milner had given Villa a fifth-minute lead from the penalty spot. However, much to the frustration of Martin O’Neill, referee Phil Dowd did not send off Nemanja Vidic for his foul on Gabriel Agbonlahor, and the Villa boss described the incident as the turning point of the game.
“It’s so straightforward it’s incredible,” O’Neill said. “It’s plain for all to see, it’s an inexplicable decision and I don’t understand it. It’s a goalscoring opportunity. He’s felled in the penalty area.
It’s straightforward from an otherwise fine referee who has got it wrong. It’s as simple as that.”
Ferguson admitted Vidic “was probably lucky” not to be dismissed, but concentrated on celebrating an incredible 32nd major trophy as United manager. “Winning this trophy is special to us,” he said.
“You’re in this game to win and I appreciate everything we have achieved as a club and I appreciate the luck I’ve carried. That’s important.
“In the main we were the better team but credit to Aston Villa’s performance. In the last 10 minutes when they started shoving up that big brigade of theirs it was like the Alamo. They had a go. Dunne had a back post header and missed altogether. You need a bit of luck in these situations.”
Villa, hunting a sixth League Cup triumph, started like a train and caught United on the hop inside four minutes. Ashley Young flicked the ball through to Agbonlahor, whose pace took him beyond Vidic, only to be tugged back by the Serb.
Dowd pointed to the spot but kept his cards in his pocket before Milner sent Tomasz Kuszczak the wrong way from the spot.
Villa began to look comfortable but seven minutes later United were level. Dimitar Berbatov robbed Richard Dunne and raced towards goal. Dunne got in a timely challenge but the ball rolled to Owen, who calmly stroked home from 18 yards.
That appeared to spur United and Ji-Sung Park hit a post in first-half injury time, while Brad Friedel saved well from Michael Carrick just after the break. But on 74 minutes United eventually broke through.
Man-of-the-match Valencia played a one-two with Berbatov and chipped over a cross for Rooney to plant a header over the out-stretched Friedel and into the corner. Rooney hit a post with another header from an identical Valencia cross just four minutes later, while Villa also hit the woodwork in a frantic late surge – Stuart Downing’s cross coming off the head of Vidic and going behind for a corner – but United held on.