Brady overcame two interceptions in engineering a comeback from a 10-0 deficit, hitting Wes Welker 10 times for 88 yards and a score as the Patriots (11-4) emerged with the win.
Stevan Ridley ran for 84 yards on 18 carries and Patrick Chung came up with a pair of late-game interceptions to secure New England's victory.
The Jaguars (2-13), meanwhile, remained on track for the worst season in franchise history despite a 348-yard passing performance from Chad Henne.
Justin Blackmon provided Jacksonville's lone touchdown, gaining 79 yards on seven catches.
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