The sixth-year 49ers quarterback said he opted to kneel rather than remain seated as he did last week "to show more respect for men and women who fight for the country."
He was joined by his teammate, safety Eric Reid, who knelt beside the quarterback before the game between the San Francisco 49ers and San Diego Chargers.
It was the Chargers' 28th Annual Salute to the Military night, and most of the fans on hand booed Kaepernick, who said he would continue to take a knee in future games.
"As far as how long this goes, I'm not sure," he said in a post-game news conference. "I want to be able to affect change and I think there are a lot of other people who do as well."
Former NFL player and Green Beret Nate Boyer, a guest of Kaepernick, stood to the quarterback's left with his right hand over his heart.
Prior to the game, Kaepernick, Reid and Boyer had discussed ways to show respect for the military while also protesting racial issues in the country. And they arrived at taking a knee, the quarterback said.
Before the game, Petty Officer 1st Class Steven Powell from the US Navy sang "The Star-Spangled Banner." Fans in the sparse crowd chanted "U-S-A! U-S-A!" after Powell concluded.
When Kaepernick lined up to begin the game, the crowd in San Diego booed. They booed before every snap of his 16 plays.
Kaepernick led the team to a touchdown on an 85-yard drive and the 49ers beat the Chargers 31-21.
He had some supporters in the crowd, though. Kaepernick signed autographs before the game and when No. 7 in a 49ers jersey loped out for warmups, many people in red 49ers jerseys clapped and cheered.
Kaepernick: 'I love America'
Kaepernick, who is biracial, has said he would refuse to stand during the song because he will not "show pride in a flag for a country that oppresses black people and people of color."
In a post-game news conference Thursday, Kaepernick said his motivations had been misconstrued by the media.
"The media painted this as I'm anti-American. I'm anti-men and women of the military," the quarterback said. "That's not the case at all."
"I realize men and women of the military go out and sacrifice their lives, put their selves in harm's way for my freedom of speech and my freedoms in this country, my freedom to take a seat or take a knee," he said. "I have the most utmost respect for them. And I think what I did was taken out of context and spun a different way."
Kaepernick said he intended to donate the first $1 million he earns this year to different organizations that help communities, although he did not name specific ones.
"I'm not anti-America," he said. "I love America. I love people. That's why I'm doing this. I want to help make America better."
Farther north in California, Seattle Seahawks cornerback Jeremy Lane sat during the national anthem prior to the game against the Oakland Raiders. He told reporters that he felt similarly to what Kaepernick had expressed and wanted to show support for him.
"I don't mean no disrespect to anybody, but I'm just standing behind what I believe in," Lane said.
Seahawks head coach Pete Carroll was asked about Lane's actions.
"It's totally an individual decision," Carroll said. "This is very -- very interesting issues that we're dealing with right now. Our team has been working at it. We've been in the process of communicating about a lot of stuff right now. That was an individual thing.
"But I'm really proud of the progress we're making in the conversation, and I look forward to continue it with our guys," he said. "It's really important to us to understand and to be smart about what we're doing and how we handle our business, and, like I've been telling you, we have a great group of guys that lead this team, and they're going to help us as we move forward. I'm very much in support of them in how we handle it. This was an individual statement tonight."
Carroll said he talked to Lane after the game about not standing for the anthem, saying that his cornerback was composed and poised.
"The individuals in this program have always been very crucial to us, and recognizing them," Carroll said. "This is another time we support our guys."
The complexity of the situation was not lost on those tailgating before Thursday's game.
A 49ers fan told CNN, "He's got the right to do what he wants as an American. I just feel that as an American, we should respect our country and our flag. There are other ways for him to do it, so I have mixed emotion and mixed feelings about it."
Meanwhile, a Chargers fan said, "It's sad for all the military people who have given their lives, and who are thinking of giving their lives for our freedom, for his right to do that and to disrespect the flag and everything that it stands for, but then again, that's what they fought for so he would have his right."
Kaepernick addresses socks
Kaepernick also addressed the saga of his socks after the game. Photos had surfaced on social media of him wearing socks that depict pigs in police hats.
"We have cops that are murdering people. We have cops in SFPD that are blatantly racist. Those issues need to be addressed," he said.
"I have uncles, I have friends that are cops. I have great respect for them because they are doing it for the right reason and they genuinely want to protect and help people," he said. "That's not the case for all cops. And the cops that are murdering people and are racist are putting other cops in danger -- like my family, like my friends."
According to USA Today
, Kaepernick wore the socks as early as August 10. USA Today also reported that the head of a national police organization ripped Kaepernick for the socks, saying the quarterback is "dishonoring police officers with what he's wearing on the field."
"It doesn't seem like he's thought through or bothered to educate himself about the way (law enforcement officers) are out there trying to do a very difficult job and the vast majority of the time get the job done right," said Bill Johnson, who is the executive director of the National Association of Police Organizations.
Kaepernick addressed the socks in an Instagram post on Thursday afternoon, explaining that he began wearing them before he took a public stance on the anthem.
He didn't wear the socks during the game.