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It was the second time this preseason that Kaepernick has sat during the anthem.
After the game, during an interview with NFL.com, Kaepernick explained that the move was a protest over how the country treats black people and people of color.
"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 said. "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."
Kaepernick went on to explain that he did not tell the 49ers of his intentions to protest the anthem and flag, noting that he wasn't going to seek out approval for something he felt he needed to do.
"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."
The 49ers issued a statement explaining that they respect Kaepernick's decision to protest the anthem, but also acknowledge that the anthem is a ceremony that honors the very liberties that give Kaepernick the right to protest.
"The national anthem is and always will be a special part of the pre-game ceremony. 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 and participate, or not, in our celebration of the national anthem."