Kaepernick outperformed Robert Griffin III in the first matchup of two of the game’s young, agile quarterbacks, both of whom have struggled this season after breakout years in 2012.
Kaepernick threw two TDs to Anquan Boldin and one to Vernon Davis. Boldin finished with 94 yards on five catches.
The 49ers improved to 7-4 and tied for second with Arizona in the NFC West.
Griffin was 17 for 27 for 127 yards, threw one interception and was sacked four times.
The Redskins fell to 3-8.
Heading into the fourth quarter, the QB that led the 49ers to last season’s Super Bowl was 13 for 21 for 212 yards with no interceptions.
It was quite a change from what he’s been doing. In a Week 1 victory over Green Bay, Kaepernick threw for 412 yards.
But in the nine games since, he’d reached 200 yards passing only once – including a combined 218 over the past two games. San Francisco was held under 200 net yards in each of those defeats.
So Kaepernick, like Griffin, has been under a lot of scrutiny lately, but he at least showed signs of improvement.
Not so for RG3. His first four passes fell incomplete. His fifth was caught for a 1-yard loss. And his sixth was picked off.
The 49ers then drove to Phil Dawson’s 29-yard field goal that made it 10-0 with 12:09 left in the second quarter.
That’s when Griffin and the Redskins finally put together a couple of sustained drives – and finally got on the scoreboard.
A 13-play possession, followed by an 11-play possession, resulted in field goals by Kai Forbath.
The first came from 36 yards with 6:43 left in the second quarter, and the other was from 35 yards on the last play of the half after some scrambling to get the kicking unit on the field with no timeouts left.
After opening 1 for 6, Griffin went 9 for 11 for 85 yards in the second quarter.
Kaepernick was 6 for 10 for 118 yards and the TD in the first half. He was sacked once on each of San Francisco’s first two possessions, which both ended with punts. But the Niners’ third drive went 62 yards over seven plays for a score.
The final two plays were Kaepernick-to-Boldin, first for 24 yards, then for 19 to make it 7-0 with 3:19 left in the first quarter. Cornerback Josh Wilson was beaten on both – as he was repeatedly throughout the game.
Washington’s first three possessions were three-and-outs, with everyone watching how Griffin would fare after several days of focus on the reigning NFL Rookie of the Year.
His willingness to take his fair share of blame publicly was a major topic of conversation, as was his relationship with coach Mike Shanahan and Shanahan’s son, offensive coordinator Kyle.
Perhaps the most surreal moment of all came during a midweek news conference, when – prompted largely by comments from receiver Santana Moss – Griffin found himself discussing the merits of proper pronoun usage, saying: “Maybe I can say ‘I,’ ‘me’ a whole lot more, but other people can take that the wrong way, too.”
The elder Shanahan’s job stability also has been a popular issue this week, because the Redskins could be on their way to a third last-place finish in his four years. He has one season remaining on a $35 million, five-year contract.