The in-form striker opened the scoring in the first half and claimed an assist for Frank Lampard's strike during a 2-1 triumph.
Michael Carrick's withdrawal left Chris Smalling, Tom Cleverley, Danny Welbeck and Rooney to represent the Reds at Wembley with Welbeck starting in a wide role on the left.
Rooney had a header spectacularly tipped away by Julio Cesar in the 10th minute but he was penalised for a push and the hosts conceded a penalty when Jack Wilshere was adjudged to have handled a Ronaldinho cross. Ronaldinho's spot-kick was saved by Joe Hart, who also stopped the rebound and Cleverley dived in to save a certain goal by thwarting Neymar.
Welbeck stabbed over the bar following a neat move involving the impressive pair Rooney and Wilshere before Rooney netted in the 26th minute, pouncing to stroke into the net after Julio Cesar kept out Theo Walcott.
Cleverley made way for Lampard at the break and the Chelsea midfielder restored the lead after Fred had levelled for the South Americans, punishing an error by Gary Cahill. Collecting a pass from Rooney, the veteran campaigner steered a superb shot past Julio Cesar and in off an upright.
Welbeck was then replaced by James Milner after a typically lively performance while Smalling made a vital late clearance when Neymar's cross looked to pick out Fred as England picked up only a fourth-ever win against the Brazilians.