The only jerseys selling better were the Dallas Cowboys rookie running back Ezekiel Elliot's and New York Giants wide receiver Odell Beckham Jr's.
Kaepernick was lambasted late last month after he came out publicly saying he would not stand for the national anthem because he said he didn't want to show pride in a flag of a country "that oppresses black people and people of colour".
While Kaepernick has been heavily criticised for his protest, he has also received support. He was joined in his protest by 49ers safety Eric Reid.
"I'm not anti-American," Kaepernick said after the game. "I love America. That's why I'm doing this."
Earlier this morning, President Barack Obama commented on Kaepernick's stance at the G20 Summit.
"He's exercising his constitutional right to make a statement," he said. "I think there is a long history of athletes doing so."
Kaepernick, who is being paid $NZ16.3 million this year, will begin the season as the backup to Blaine Gabbert.