"How can you stand for the national anthem of a nation that preaches and propagates, 'freedom and justice for all,' that is so unjust to so many of the people living there," he said at Saturday's ceremony.
Other players joined his protest in the 2016 season, drawing the ire of President Donald Trump, who called for team owners to fire such players.
In response to the player demonstrations, the NFL agreed to commit $90 million over the next seven years to social justice causes.
Kaepernick wasn't signed for the 2017 season following his release in San Francisco.
Reid, a safety who is now a free agent, continued Kaepernick's protests by kneeling during the anthem last season. Reid has said he will take a different approach in 2018.
Kaepernick paid tribute to his friend for his own role in the protest movement.
"Eric introducing me for this prestigious award brings me great joy," he said.
"But I am also pained by the fact that his taking a knee, and demonstrating courage to protect the rights of black and brown people in America, has also led to his ostracisation from the NFL when he is widely recognised as one of the best competitors in the game and in the prime of his career."
AP
