Brady improved his playoff record to 11-1, completing 22 of 34 passes for 212 yards. The three-time Super Bowl-winning quarterback will guide the Patriots against San Diego in the divisional round next Sunday.
The Jets took an early 10-7 lead, but Brady marched New England 56 yards in 10 plays to a 20-yard field goal by Stephen Gostkowski, and then helped put together an 80-yard march that ended in a one-yard touchdown pass to Daniel Graham.
It was New England's ninth straight home playoff win.
Jabar Gaffney caught eight passes for 104 yards and Gostkowski contributed three field goals.
New York's Chad Pennington completed 23 of 40 passes for 300 yards and a touchdown, but the Patriots dominated the second half.