The protracted debate in the N.F.L. over players protesting racial injustice during the national anthem reignited with force on Friday as President Trump rekindled his war with the league over the issue and the league’s commissioner, Roger Goodell, issued his strongest support yet for the players seeking to fight racism and police brutality.

In an swift response to a video montage featuring star players asking the league to address systemic racism, Goodell said he apologized for not listening to the concerns of African-American players earlier and said he supports the players’ right to protest peacefully. During the 2016 season, Colin Kaepernick started the movement within the league when he knelt to call attention to racial injustice and violence by police, but no team has offered him a contract since then.

Goodell did not directly name Kaepernick in his video. Still, his comments were diametrically opposed to those made by the president. Trump defended New Orleans Saints quarterback Drew Brees, who said this week that it was disrespectful to kneel during the pregame playing of the “The Star-Spangled Banner.”

After a swift rebuke from fellow N.F.L. players, including some of his teammates, Brees apologized on Thursday. But the president said on Twitter that Brees should not have bowed to pressure and everyone should stand when the national anthem is played.

“We should be standing up straight and tall, ideally with a salute, or a hand on heart,” the president wrote. “There are other things you can protest, but not our Great American Flag — NO KNEELING!”

Trump first attacked the N.F.L. over protests during the national anthem in September 2017. During a campaign rally, he called on owners to fire any players who knelt during the anthem, and used a vulgarity to describe quarterback Colin Kaepernick, who started the movement when he knelt through the previous season to call attention to racial injustice and police brutality.

Kaepernick adopted the kneeling gesture on the advice of a former Green Beret he had met, who suggested it would be a respectful way to call attention to his cause.

A spokesman for the N.F.L. declined to comment on the president’s comments about Brees and the national anthem.

The president’s admonishment comes as the N.F.L., like the rest of the country, grapples with how to respond to the killings of black Americans at the hands of police, and to the protests that have engulfed the nation for nearly two weeks since the death of George Floyd in Minneapolis.

More than any other major sports league, the N.F.L. has wrestled in recent years with the issue of race, the lack of African-Americans and other people of color in positions of power in the league and the rights of players to protest social issues on the field. While three-quarters of the league’s players are African-American, nearly every owner is white and several of the most prominent owners are strong supporters of the president.

In this latest wave of civil unrest, many players, coaches and owners have spoken out against racism, and have pledged to become more involved in finding solutions.

Last Saturday, Roger Goodell was the first big league commissioner to issue a statement of concern in response to Floyd’s death, but his words were panned as hypocritical because of the league owners’ rejection of Kaepernick, who has not found another job in the league since the end of the 2016 season.

On Thursday, some of the league’s biggest stars, including Kansas City Chiefs quarterback Patrick Mahomes, released a video calling on the league to condemn the oppression of black people and to apologize for not supporting players who protested peacefully.

On Friday, the N.F.L. also tweeted the video that the players made and said, “Players, we hear you.”

Soon after, Goodell responded with his own video in which he made his strongest and most specific support of the demands and goals of African-American players. In the one minute, 21-second video, the commissioner condemned the oppression of black people, apologized for not listening to the concerns of African-American players and encouraged the league’s athletes to protest peacefully.

After offering his condolences to “the families who have endured police brutality,” Goodell said that “We, the National Football League, condemn racism and the systematic oppression of black people.”

In an apparent allusion to Kaepernick, who settled a grievance with the league last year in which he accused the league of blackballing him because of his political protests, Goodell added: “We, the National Football League, admit we were wrong for not listening to N.F.L. players earlier and encourage all to speak out and peacefully protest.”

“We, the National Football League, believe black lives matter,” he added. “I personally protest with you and want to be a part of the much-needed change in this country. Without black players, there would be no National Football League.”

In earlier statements, Goodell has pointed to the league’s social activism campaign, Inspire Change, which has donated tens of millions of dollars to groups working in communities and pushing for the eradication of social injustice.

But given the political volatility of the issue of the national anthem, Goodell’s statement in support of peaceful protests could inflame the relationship between the league and the president, who has used the issue of protests during the national anthem to galvanize his supporters.

After the president first criticized the N.F.L. for not cracking down on protesters, owners voted to tighten the league’s policy to prohibit players from kneeling during the national anthem. After the N.F.L. Players Association filed a grievance to reverse the policy, the league backed off and has never penalized a player for protesting.

Now, Goodell has spoken in support of the players’ right to protest and many more players have publicly called for the need for action against racism and police brutality. Some players, including running back Adrian Peterson, have already said they intend to kneel during the national anthem this coming season, which does not begin until September.

While the commissioner has pledged to listen and “move forward together for a better and more united N.F.L. family,” he will have to convince owners, broadcasters, sponsors and fans who are uncomfortable with player protests, experts said.

“What he needs to articulate to people who buy commercials and own teams and anyone who might push back against the players is, are there things they are doing that are negative?” said Charles K. Ross, the author of “Outside the Lines: African Americans and the Integration of the N.F.L.” “You can also stand up to individuals who are going to push back and remind them we have the First Amendment.”