Kaepernick, who finished the day 1 of 5 with four yards passing, entered the game at full strength and fresh off last week's 296-yard performance. Over his last four games (not including Week 13 vs. Bears), he's 86 of 145 for 1,110 yards with eight TDs and two interceptions.
When asked after the game about the decision to sit Kaepernick, coach Chip Kelly said, "I thought we needed a spark."
The quarterback said he was surprised when quarterbacks coach Ryan Day informed him he has been benched.
"I was surprised. It wasn't something I expected ... It's not my place to really argue on the sideline," Kaepernick said. "I want to make sure I do what I can help this team win and that was the decision that was made so I'm going to support my teammates."