For the second week in a row, the 49ers had more than 20 players kneeling during the national anthem with their hands over their hearts. Teammates stood behind the kneeling players with one hand on a kneeling teammate's shoulder and the other over their hearts.
The Colts wore black T-shirts with the words "We Will" on the front and "Stand for equality, justice, unity, respect, dialogue, opportunity" on the back for the second straight week. The players stood with their arms locked during the anthem.
Pence tweeted a statement in which he said he would not dignify any event that disrespects soldiers, the flag or the anthem.
On Sunday afternoon, President Donald Trump said he had asked Pence to leave the game if any players knelt during the anthem.
49ers safety Eric Reid said he believed Pence's actions were premeditated.
"First of all, does anyone know the last time he's been to a football game?" Reid said after the game. "OK, with that being said, he tweeted out a 3-year-old photo of him at a Colts game. So with the information that I have, the last time he's been to a football game is three years ago. So this looks like a PR stunt to me.
"He knew our team has had the most players protest. He knew that we were probably going to do it again. This is what systemic oppression looks like. A man with power comes to the game, tweets a couple things out and leaves the game in an attempt to thwart our efforts. Based on the information I have, that's the assumption I made."
A former governor of Indiana, Pence had been in Indianapolis as part of the celebration of Peyton Manning and his jersey retirement and induction into the Colts' Ring of Honor during Sunday's game.
Pence had tweeted a photo of him and his wife, Karen Pence, saying they were looking forward to cheering for the Colts and honoring Manning. But the Indianapolis Star noted that the photo appeared to be from 2014.
The photo the vice president tweeted showed him wearing a Colts polo shirt. He was photographed wearing a suit during the national anthem Sunday.
The pool reporter with the vice president had been told to stay outside the stadium and that Pence might leave the game early.
Aides to the vice president did not respond to questions on whether he had planned to make the public walk-out in the game against the 49ers, who have regularly held the demonstrations.
Pence has attended other NFL games, including December's Colts-Jets game at MetLife Stadium when he was the vice president-elect.
The NFL and the Colts declined to comment on Pence's exit, while Indianapolis coach Chuck Pagano steered clear of the topic in his postgame news conference.
NFL players who have demonstrated during the national anthem over the past year have said they are protesting police brutality and racism, not the flag or the anthem itself.
The protests began in August 2016, when former 49ers quarterback Colin Kaepernick sat during the national anthem in a preseason game.
During a rally in Alabama on Sept. 22, Trump chastised the practice, saying, "Wouldn't you love to see one of these NFL owners, when somebody disrespects our flag, to say, 'Get that son of a bitch off the field right now, out, he's fired.'" He later encouraged fans to leave NFL stadiums if they saw it happen in front of them.
Reid said the 49ers' actions during the anthem Sunday were not as planned as last week's display in Arizona.
"These were guys that felt compelled to continue to protest. I think it is gaining ground," Reid said. "... I will continue to say and encourage people to educate themselves on how we got to where we are today because it didn't happen overnight and it's not going to happen overnight to fix these issues. So we're going to keep talking about it. I know that I will keep doing what I feel is necessary to use the platform I have to make those changes.
"It's really disheartening when everything that I was raised on was to be the best person I could be to help people that need help and the vice president of the United States is trying to confuse the message on what we're trying to put out there. I don't know what else to say about it."
Around the NFL on Sunday, at least seven players from two teams knelt during the national anthem while three Miami Dolphins players and the Tennessee Titans' Rishard Matthews remained in the tunnel or locker room for the anthem. Oakland Raiders running back Marshawn Lynch continued to sit during the anthem.
The Associated Press contributed to this report.