The Panthers couldn't answer, failing to score in the second half.
The 49ers took a 13-10 lead into the locker room after Vernon Davis caught a 1-yard touchdown pass in the back of the end zone from Kaepernick with 5 seconds left in the first half.
Davis was initially ruled out of the end zone on a play where 49ers coach Jim Harbaugh raced on to the field, drawing a 15-yard penalty for unsportsmanlike conduct. Harbaugh said he wasn't disputing the catch, but rather that the play clock continued to run after the play.
All turned out fine for the 49ers though, as officials overturned the call ruling Davis dragged his left foot and scored.
Television replays showed the 49ers had 12 men in the huddle with backup tight end Vance McDonald racing to the sidelines before the ball was snapped. Referee Carl Cheffers defended the call telling a pool reporter the ball hadn't been spotted — although Fox television replays seem to indicate otherwise.
Carolina spotted San Francisco a 6-0 lead with two defensive penalties — an unnecessary roughness on safety Mike Mitchell and a headbutt on cornerback Captain Munnerlyn — leading to field goals.
NOTES: It's the second time since 2008 the Panthers lost at home in the divisional playoffs after winning the NFC South and claiming a first-round bye with the No. 2 seed. ... 49ers FB Will Tukuafu left with a leg injury in the first half and didn't return.