The incident happened as the judges analyzed Lochte's foxtrot routine with his partner Cheryl Burke. Two men wearing anti-Lochte shirts walked onto the dance floor, according to ABC.
Security tackled the men to the ground, and they were removed from the stage.
Judge Carrie Ann Inaba was heard telling someone to "back off," but the camera stayed fixed on her.
Photos showed two men wearing anti-Lochte shirts with their hands behind their back. ABC said four to five other women were escorted out of the audience after chanting against Lochte.
AIR7 HD captured the protesters being taken into custody. Police said the men, identified as 48-year-old Sam Sododeh and 40-year-old Barzeen Soroudi, both of Los Angeles, were booked for trespassing.
According to Los Angeles police, Sododeh and Soroudi had valid tickets to the show and wore the anti-Lochte shirts under their clothing.
Lochte expressed his concern over the incident.
"We thought it was a joke, something prior to the show, you know. Then, when we realized it wasn't, that hurt. It broke my heart that people are still on that subject and no one is moving forward," he said.
The protest comes after Lochte and his U.S. Olympic teammates were involved in a drunken dispute in Rio de Janeiro, Brazil.
Lochte and his teammates claimed that they were robbed and threatened by men with guns, but Lochte later admitted that he "over-exaggerated" the story.
Upon returning to the U.S., Lochte lost all four of his sponsorships and was suspended from the U.S. Olympic team for 10 months.