New England jumped out to a 17-0 lead in the first quarter, when Kevin Faulk scored touchdowns on an 11-yard run and a 43-yard pass from Brady.
New England's lead was 27-0 at the half.
Brady completed 16 of 23 passes for 109 yards for the Patriots (10-4), who made an impressive comeback after a 21-0 loss at Miami last Sunday.
David Carr was 16-for-28 for 127 yards, no touchdowns and four interceptions, and Ron Dayne scored once on 18 carries for 94 yards for the Texans (4-10), who suffered the fourth loss in the last five games.
New England had four interceptions.