The 49ers (7-4) were clinging to a 10-6 lead at halftime but came out strong after the break as Kaepernick hooked up with Anquan Boldin on a 6-yard TD pass following a six-play, 59-yard drive.
Kaepernick finished 15-of-24 for 235 passing yards and Boldin made five grabs for 94 with a pair of scores for San Francisco, which snapped a two-game slide.
Robert Griffin III was held without a touchdown, completing 17-of-27 passes for 127 yards with an interception for the Redskins (3-8).
He also picked up 22 rushing yards on six carries.
Celebrity Breakups and divorces of 2014 [PHOTOS]