Brady racked up 320 passing yards, helping the Patriots (11-3) rally from a 16-7 deficit early in the second quarter with 27 straight points.
The Pats claimed their ninth division crown in 11 years with help from Aaron Hernandez, who made nine grabs for 129 yards and a score.
Tim Tebow, who has led the Broncos to five fourth-quarter comeback wins in eight weeks, couldn't pull off another miracle despite two rushing TDs and 194 aerial yards on 11-of-22 passing.
Denver (8-6) remained in first place in the AFC West despite the loss thanks to Oakland's last-minute loss to Detroit Sunday.
Swim Week Miami Beach 2014 [PHOTOS]