Rooney, who came on as a substitute, scored with a superbly executed header after 74 minutes for his 20th goal in his last 20 matches as United became the first team since Nottingham Forest in 1989 and 1990 to win the cup in successive seasons.
"It's a great feeling to play a final at Wembley and score the winning goal," Rooney told the BBC.
"I think all the players who played in the competition should be proud of themselves. I wanted to play but had a bit of a sore knee."
Aston Villa, the first winners of the trophy in 1961, took the lead after five minutes when James Milner scored from the penalty spot, but were often second best for long periods against United who also hit the post twice.
Michael Owen brought United back into the match with a 13th minute equaliser, swept home with a sweet first touch which would have impressed the watching England manager Fabio Capello.
However, Owen limped off after 42 minutes with a hamstring injury with Rooney coming on in his place.
United went close to scoring when Ji-Sung Park hit the post at the end of the first half and Rooney headed against the post two minutes after scoring. Villa also hit the woodwork when an Emile Heskey header bounced off the United bar late in the game.
