His teammate, San Francisco 49ers safety Eric Reid, kneeled beside him in solidarity prior to the game.
Following the game, Kaepernick told reporters: “We were talking to him [Reid] about how can we get the message back on track and not take away from the military, not take away from pride in our country but keep the focus on what the issues really are.
“As we talked about it, we came up with taking a knee because there are issues that still need to be addressed and there was also a way to show more respect for the men and women that fight for this country."
Kaepernick's protest is spreading, Seattle Seahawks cornerback Jeremy Lane also refused to stand during the anthem in a game against the Oakland Raiders Thursday.
Thursday night's game in San Diego was billed as "military night,” a tribute to the hundreds of thousands of military personnel who live in a city well known for its patriotism and military bases. As soldiers spread the flag colors across the field during the anthem, Kaepernick and Reid could be seen kneeling.
Kaepernick took the field wearing plain white socks, which is significant because since August 10 he had been wearing socks with a cartoon image of pigs wearing police officer's caps.
Although he was widely booed during the game, some fans asked for his photo and autograph.
Following the game, he told reporters: “I'm not anti-American. I love America. I love people. That's why I’m doing this. I want to help make America better, and I think having these conversations helps everybody have a better understanding of where everybody is coming from.
“Those conversations are important to have because the better we understand each other, the better we know each other, the better we can deal and communicate with each other which ultimately makes everyone, puts everybody in a better position."
The controversial quarterback also said that he plans on donating $1 million to charities that support racial equality.
I’m currently working with organizations to be involved and making sure I’m actively in these communities, as well as donating the first million dollars I make this [season] to different organization to help these communities and help these people,” he told reporters.
It won’t be the first charitable contribution of his career. Earlier this year, he donated $60,000 of backpacks to students in Harlem and in the Bronx, New York.