"We were wrong for not listening to NFL players earlier and encourage all to speak out and peacefully protest," NFL Commissioner Roger Goodell said.
The NFL had banned its players from dropping to one knee, a practice started by Colin Kaepernick in 2016.
Meanwhile, a large protest is expected in Washington DC on Saturday.
The demonstration is the latest in a series of protests against racial discrimination that have been held across the US following the death of George Floyd in Minneapolis on 25 May.
Mr Floyd, an unarmed black man in handcuffs, died after a white policeman knelt on his neck for nearly nine minutes. The officer has been charged with murder while three colleagues stand accused of aiding and abetting.
On Friday, Minneapolis officials said police would be banned from using neck restraints and California pledged to follow suit.
In a video, Mr Goodell denounced racism in the US in comments that came shortly after a number of players urged the NFL to take a stronger stance on racism and police brutality in the country.
"We, the National Football League, believe black lives matter. Protests around the country are emblematic of the centuries of silence, inequality and oppression of black players, coaches, fans and staff," he said.
"I will be reaching out to players who have raised their voices and others on how we can improve."
But on Friday President Donald Trump again voiced his opposition to such protests, saying on Twitter: "We should be standing up straight and tall, ideally with a salute, or a hand on heart. There are other things you can protest, but not our Great American Flag - NO KNEELING!"
What's the story behind Kaepernick's kneeling?
The practice of kneeling during the customary pre-game playing of the national anthem was started by black player Colin Kaepernick in 2016 in protest against racial injustice.
A number of other players soon joined Kaepernick, who was a quarterback for the San Francisco 49ers at the time.
He became a free agent after the 2016 season and remains unsigned. Kaepernick filed a grievance against NFL owners in October 2017, believing they were conspiring not to hire him because of his kneeling protests.
The two sides resolved the grievance in February under a confidentiality agreement.
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