After starting as a substitute, Rooney was only on the pitch because of an injury to Michael Owen, who had levelled James Milner's fourth-minute penalty.
He was not going to let that inconvenience stop him becoming the Wembley match-winner against Aston Villa though.
And 16 minutes from time, Rooney got on the end of Antonio Valencia's cross and looped home yet another headed goal - his fifth in a row - to take his goal tally for the season to 28 and allow United to retain the trophy after a thrilling Wembley encounter Sir Alex Ferguson feared was not possible.
One of the more obvious reasons why Ferguson would choose to leave his best player out of such a showpiece occasion was the surface, which has been claggy every time the Red Devils have played at the rebuilt stadium.
Fearing a draining match, plus extra-time, then an England game and a Premier League trip to Wolves, when victory will take his side top, before that decisive meeting with AC Milan on March 10, Ferguson presumably felt this was an outing Rooney could do without.
Yet any worries about the pitch were groundless. And Villa's flying start meant there was no chance of either side being allowed to turn this into the sterile affair many had predicted.
At the time, Martin O'Neill questioned how Nemanja Vidic avoided a card of any kind for his foul on Gabriel Agbonlahor.
As the contest wore on, and an increasing number of his own players ended up in Phil Dowd's notebook, the criticism grew.
If Agbonlahor had gone down when Vidic first grabbed his shirt, the card could have been red.
Instead, the Villa striker admirably attempted to stay on his feet after outpacing the Serbian to reach Ashley Young's lofted pass beyond the United defence.
In the end, it was too much. Vidic stuck out a leg and hauled Agbonlahor down. Milner kept his nerve, sending Tomasz Kuszczak the wrong way to provide the contest with the start it craved.
As tends to be the case when they fall behind, United's response was an all-out attacking assault, which in turn provided Villa with space to counter.
The mixture produced a thrilling spectacle, made all the more absorbing because Ferguson's team levelled so quickly.
So solid all season, it was just Richard Dunne's luck his blunder should come in Villa's biggest game of the year.
The Irishman was robbed by Dimitar Berbatov close to his own penalty area and though he made up the ground, in making his despairing tackle, Dunne only succeeded in rolling the ball into Owen's path, offering the kind of instinctive first-time finish he has made a career out of.
That Owen's contribution - and Rooney's exile - came to an end three minutes before the break was cause for regret, although the watching Fabio Capello has long since deduced those dodgy hamstrings cannot be trusted through another World Cup campaign.
Capello was probably also reaching the conclusion Stephen Warnock should be handed his problematic left-back berth against Egypt on Wednesday.
But when Warnock slipped just before half-time, man-of-the-match Valencia galloped past him down the by-line, his cross eventually arriving at the feet of Park Ji-sung, who slammed it onto the inside of a post, where it rocketed across goal for Carlos Cuellar to hack clear.
Friedel palmed away a magnificently constructed effort from Michael Carrick after half-time, although Villa were United's equals and could easily have levelled when Ashley Young sent a volley bouncing into the ground.
The problem for Villa was knowing Rooney lurked.
After falling victim to him in midweek, Gianfranco Zola claimed England's superstar has the Midas touch.
It is more a Boy's Own story he is writing at the moment.
Having looped home yet another header to put his side ahead, Rooney came agonisingly close to making it number six when he crashed another onto the woodwork.
Villa responded in kind, Vidic nudging Emile Heskey's header onto his own bar. But that would have spoiled the story.