SAN DIEGO — Colin Kaepernick began the game by taking a knee during the national anthem. The veteran quarterback ended it with reason to hope he’ll have more games with the San Francisco 49ers.

Kaepernick passed for 103 yards after kneeling in protest alongside teammate Eric Reid during the national anthem in the Niners’ 31-21 preseason victory over the San Diego Chargers on Thursday night.

Kaepernick and Reid, a starting safety who wasn’t playing, declined to stand for the anthem before a preseason game dedicated to military appreciation by the Chargers. Kaepernick has decided not to stand this season to draw attention to American racial injustice, minority oppression and a litany of additional concerns ranging from police brutality to military veterans’ rights.

“The message is that we have a lot of issues in this country that we need to deal with,” Kaepernick said. “We have a lot of people that are oppressed. We have a lot of people that aren’t treated equally, that aren’t given equal opportunities.”

Kaepernick then played a solid first half in his competition for the 49ers’ starting job, going 11 for 18. The veteran didn’t have an interception or a touchdown pass, missing on two potential scoring throws in the waning seconds of the half. He also rushed four times for 38 yards.

Less than four years after leading the 49ers to the Super Bowl, Kaepernick is in competition for the starting job with Blaine Gabbert, who didn’t play in San Diego after getting extensive playing time in the first three preseason games for the Niners (2-2).

Kaepernick hopes to be the 49ers’ starter, but he is likely also in competition for a roster spot after a disappointing 2015 season during which he lost his starting job and had extensive injury problems. Although Kaepernick realizes he still could be released, he’s hopeful of a future with the Niners.

“This is a phenomenal organization, and I’ve had great conversations here,” Kaepernick said. “I’ve had great memories here, and this team has given me the opportunity to become the man I am today. I’m grateful for that. I’m thankful for that, and San Francisco has become my home.”

Niners coach Chip Kelly wouldn’t say whether Kaepernick’s play had improved his chances to win the starting job — or to avoid being cut.

“We’ll make those decisions when we watch the film,” Kelly said. “That goes for everybody on the football team, not just Colin.”

Kaepernick didn’t play in the current preseason until last week against Green Bay, when his refusal to stand for the anthem first gained attention.

Kaepernick got only scattered boos before the game and during the anthem, but Chargers fans serenaded him while he led a 16-play, 85-yard scoring drive to open the game capped by DuJuan Harris’ 1-yard TD run.

Christian Ponder passed for 101 yards and rushed for the go-ahead touchdown for San Francisco with 3:08 to play, improving his own chances for a prominent job in the Niners’ fluid quarterback picture.

Marcus Rush got his fifth and sixth sacks of the preseason in the second half of a standout performance by the San Francisco linebacker. After Rush forced a fumble that led to Ponder’s TD run, he intercepted a deflected pass.

Kelvin Taylor sealed the Niners’ win with a 10-yard TD run with 1:55 left.

Kenneth Farrow rushed for 63 yards and a third-quarter touchdown for the Chargers (1-3), who rested their stars. Isaiah Burse caught a 17-yard TD pass from Mike Bercovici in the third quarter during strong performances by both roster hopefuls.

Chargers fullback Chris Swain, a rookie from Navy, also scored on a 2-yard run in the second quarter.

Farrow excelled in his competition for the third-string running back job, breaking off a 44-yard run on a third-quarter drive. He is hoping to secure a role after Branden Oliver was lost for the season with an Achilles tendon injury.

“I definitely had to step up tonight, being that there is a hole in the room,” Farrow said. “I feel like I did a good job, and we’ll see what happens.”

ROOKIE WATCH

49ers: QB Jeff Driskel threw interceptions on his first two passes of the third quarter, certainly damaging his hopes of winning a job from Ponder or Kaepernick.

Chargers: DE Joey Bosa was on the sideline, but didn’t play. The first-round pick staged a 31-day holdout before signing Monday. … Bercovici passed for 75 yards with two interceptions.

POSITION BATTLES

49ers: CB Will Redmond appeared to have an inconsistent game in his attempt to earn a larger role. The rookie was playing in just his second preseason game after a knee ligament injury.

Chargers: Burse looked sharp in his attempt to earn a job, catching five passes for 63 yards and returning kicks.

INJURY UPDATE

49ers: No apparent injuries.

Chargers: LB Nick Dzubnar left the field slowly in the third quarter with medical personnel accompanying him. He returned to the game later.


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