"I am not going to stand up to show pride in a flag for a country that oppresses black people and people of color," Kaepernick told NFL Media after Friday's game. "To me, this is bigger than football and it would be selfish on my part to look the other way. There are bodies in the street and people getting paid leave and getting away with murder."
The 49ers acknowledged in a statement that Kaepernick sat on the team's bench during the national anthem before their game against the Green Bay Packers.
"The national anthem is and always will be a special part of the pregame ceremony," the statement said. "It is an opportunity to honor our country and reflect on the great liberties we are afforded as its citizens. In respecting such American principles as freedom of religion and freedom of expression, we recognize the right of an individual to choose to participate, or not, in our celebration of the national anthem."
Kaepernick told NFL Media that he did not tell the team he was planning to protest the national anthem.
"This is not something that I am going to run by anybody," he said. "I am not looking for approval. I have to stand up for people that are oppressed. ... If they take football away, my endorsements from me, I know that I stood up for what is right."
Kaepernick also refused to stand for the national anthem in at least one other preseason game.
Pro Football Talk initially reported that Kaepernick did not stand during the anthem. He was not asked about his decision during his postgame news conference, which was held prior to the Pro Football Talk report.
Kaepernick, who is biracial, was adopted and raised by white parents. He has been outspoken on his Twitter account on civil rights issues and in support of the Black Lives Matter movement.
Numerous high-profile athletes have spoken out about civil rights issues in the wake of gun violence throughout the United States. In July, Dwyane Wade, LeBron James, Carmelo Anthony and Chris Paul opened the ESPYS with a call for social change and an end to violence, and WNBA players wore warm-up shirts to show solidarity after shootings in Minnesota and Baton Rouge, Louisiana.
Wade's cousin, Nykea Aldridge, was killed by gunfire in Chicago on Friday, a day after Wade participated in a series of panel discussions on gun violence hosted by The Undefeated on ESPN.
Kaepernick told NFL Media that he had thought about going public with his feelings for a while but that "I felt that I needed to understand the situation better."
He joins team sports athletes including Mahmoud Abdul-Rauf and Carlos Delgado in refusing to participate during patriotic American songs. Abdul-Rauf was suspended one game by the NBA in 1996 for not standing during the national anthem, saying the United States had a history of tyranny and doing so would conflict with his Islamist beliefs. He later agreed to stand and pray silently during the song. Delgado would leave the field in 2004 during "God Bless America" in protest of the Iraq War.
Kaepernick made his preseason debut against the Packers after sitting out the first two exhibition games because of tightness in his right shoulder. Kaepernick went 2-for-6 for 14 yards and added 18 yards on four carries in the 49ers' 21-10 loss.
ESPN staff writer Nick Wagoner and The Associated Press contributed to this report.