Frank Gore scored on a 2-yard touchdown run with 2:55 left in the quarter to stretch the visitors' lead to three scores.
San Francisco had a 10-0 halftime lead on a rushing touchdown by backup quarterback Colin Kaepernick and a David Akers field goal.
The Jets' offense has struggled throughout the game, accumulating 128 total yards and committing three turnovers. Mark Sanchez has completed nine passes for 89 yards as well as throwing one interception and fumbling once.
Gore leads the San Francisco rushing attack, carrying 17 times for 45 yards. Kendall Hunter has 31 yards on three carries. Alex Smith has completed 12 of 19 passes for 143 yards.
Both teams entered the game with 2-1 records.