The Manchester United striker came off the bench to turn the game with a 20 minute cameo which he rounded off in typical fashion, with a goal.
National nemesis Cristiano Ronaldo got the first for United in the last ten minutes after what had been a stale encounter.
Capello will have felt right at home as defensive tactics were the order of the day and both sides almost looked too tired to attack.
The Claret and Blue were content to wait for an opportunity from a set piece, which has been somewhat a speciality of late, but it never came.
The fisrt real chance of the game fell to the man who loves Villa Park more than any other opposition player, Ryan Giggs. He was slow to react with five minutes remaining in the first half, as Cristiano Ronaldo struck a bouncing drive which Scott Carson could only parry.
In truth the Villa keeper should of done better, but he was lucky, as Giggs could only divert it uncomfortably wide.
That was the only real action in the first half and it was not much different after the break.
United did have another chance to take the lead on 56 minutes as Nemanja Vidic rose highest at a corner, but glanced wide.
No inroads were being made by either team and it was only a matter of time before Rooney came out of hibernation.
He replaced Park Ji-Sung, who may have been unlucky. as Saha had been staring at the guillotine from the outset. The Frenchman put in a rather lethargic showing and Villa easily marked him out of the game.
By 80 minutes even Capello and the watching F.A. contingent must have been bored, but then the game came to life.
Ironically, a man who has helped put England out of a tournament or two got the opener.
Cristiano Ronaldo had been kicked, pushed and just fairly taken out of the game, mainly by England man Gareth Barry. But on 82 minutes he got his revenge as Giggs slid in a cross, which left him with an easy tap in.
The winker duly obliged and it was 1-0.
Villa didnt really threaten to force a replay, but Craig Gardner headed over just before the Claret and Blue's F.A. Cup fate was sealed for another season.
With less than five minutes remaining Rooney saw his chance to show Capello what he can do and took it. He struck the ball perfectly on the half volley past Carson from the edge of the area. Game Over.
The referee blew his whistle and United were through at the expense of Villa again. The score was slightly harsh on the home side who will have felt they should have at least claimed a replay, but with players such as Young and Agbonlahor looking tired it was one game too many.
Capello ahould not write off the Claret and Blue young guns and must take into account the hectic schedule which they have endured. They deserve a chance alongside Rooney and Co.