The two men, wearing anti-Lochte T-shirts, were arrested on suspicion of criminal trespassing, Los Angeles police spokesman Liliana Preciado said.
They had rushed the stage while Lochte was getting his scores from judge Carrie Ann Inaba for his debut performance during Monday night's live installment of the celebrity ballroom dance competition. "GMA" aired video that wasn't shown during the live broadcast of one of the men being tackled on stage by security.
"Hey, back off," Inaba said as the altercation was occurring off screen.
When the show returned, host Bergeron explained they were interrupted by "a little incident" and thanked the ABC series' security team "for staying in shape."
The video also showed at least four others in the audience wearing anti-Lochte shirts. They were escorted out while being verbally confronted by dancer Derek Hough.
Police identified the men on stage as Sam Satoodeh, 59, and Barzeen Soroudi, 25. The two were arrested on suspicion of misdemeanor trespassing and held on $1,000 bail each. A message at a number for Satoodeh was not immediately returned Tuesday. A number for Soroudi could not be found.
The two men were detained by security until police arrived to take them into custody. Preciado said police did not know what the protestors' motivations or intentions were.
No one was injured or listed as a victim in the incident, officials said.
Lochte told Bergeron that "so many feelings are going through my head right now." The swimmer added that he was "a little hurt, but I came out here. I wanted to do something I'm completely not comfortable with, and I did."
ABC did not immediately return messages seeking comment about the incident.
During the episode, the Olympic medalist performed a foxtrot routine with professional partner Cheryl Burke to "Call Me Irresponsible." They received a combined score from the judges of 24 out of 40.
Lochte and teammates have faced criticism since they were involved in an early-morning drunken encounter during the Olympics last month at a gas station in Rio de Janeiro, Brazil. They later claimed they were threatened and robbed.
United States team officials banned Lochte for 10 months, requiring him to forfeit $100,000 in bonuses and miss the 2017 world championships.