Favre was 20-of-31 for 137 and was intercepted once as the Jets (8-5) remained in a three-way tie with Miami and New England for first place in the AFC East. The loss was Favre's first ever against the Niners and snapped a four-game road winning streak for the Jets.
Thomas Jones ran for 56 yards and a touchdown that gave him 14 for the season and tied the Jets' record for TDs in a season.
A 32-yard field goal by San Francisco's Joe Nedney broke a 14-14 tie early in the fourth quarter. The 49ers (5-8) put the game away with a lengthy scoring drive capped by Hill's 3-yard TD pass to Johnson with 6:05 to play.