Rooney, on as a 42nd minute substitute for Michael Owen, headed home in the 74th minute to ensure last year's winners retained the trophy - the first time United have successfully defended a cup competition.
James Milner gave Villa an early lead from the penalty spot only for Owen, who started the game in place of Rooney, to level things up on 13 minutes with a classic strike.
But inevitably it was Rooney who grabbed the headlines, the England striker continuing his recent electric form with a 12th goal in nine games.
Villa raced out of the blocks at a soggy Wembley and took the lead in just the fourth minute, Milner sending Tomasz Kuszczak the wrong way from the spot after Gabriel Agbonlahor was upended by Nemanja Vidic in the box.
It was not the last time Vidic, who bafflingly got away without further punishment, looked suspect during a shaky first half, particularly when faced with the pace of Agbonlahor and Ashley Young.
But Villa's lead lasted just eight minutes, with Owen restoring parity soon after.
Rooney's appearance on the bench came as a surprise - he was suffering from a slight knee complaint - yet in Owen, Ferguson not only had a natural born finisher to call on, he had a player who was desperate to make an impression in what was a rare start for him.
And what an impact the striker made in front of the watching Fabio Capello. As he has on occasion this season, he rolled back the years with a tremendous finish past Brad Friedel after Richard Dunne's pockets were picked by Dimitar Berbatov.
But, just as it looked like the 'Owen for England' bandwagon was about to be fired up once again, the wheels promptly fell off as he limped off with a pulled hamstring before the end of the first half.
Nevertheless, Owen's goal had served to spark United into life, and the Premier League champions went on to enjoy the better of the opening period, despite sighters from James Milner and Emile Heskey which Kuszczak was forced to deal with.
Park Ji-sung nearly made United's slight superiority count in first half stoppage time, the South Korean's crisp strike pinging back off the upright after Stephen Warnock had slipped on the greasy turf, allowing Antonio Valencia to deliver a cross.
And United emerged for the second half in similarly determined mood, Michael Carrick's effort from the edge of the box matched only by Friedel's excellent save four minutes after the restart.
Valencia in particular was on fire after the break, and it was the Ecuadorian's lofted cross which Rooney met with a looping header over Friedel - similar to his first against Milan in the Champions League - to put United into the lead.
Rooney could have added another four minutes later - again with his head - but his downward effort from a standing position cannoned back off the base of the upright with Friedel beaten all ends up.
Villa briefly threatened to grab a late equaliser as the clock ran down, Kuszczak having to backpeddle furiously to tip a deflected cross over his crossbar on 82 minutes, but United never looked like being beaten for a second time.
So it proved as United held on to finally avenge their defeat by Villa in the 1994 final.