The Pats found themselves trailing 10-0 early in the game, but then outscored the Eagles 38-10 the rest of the way, thanks to Brady's 361 aerial yards.
Two of his scoring strikes went to Wes Welker, who made eight catches for 115 yards. Deion Branch compiled 125 receiving yards on six grabs.
BenJarvus Green-Ellis contributed two touchdown runs as New England (8-3) won its third straight game.
Vince Young connect on 26-of-48 passes for 400 yards with a touchdown and one interception for the Eagles (4-7), who fell to 1-5 at home this season.