The 20-year-old Olympic gymnast sent her "love" to Bergeron on Twitter after the television personality chided her on Monday's episode for not smiling during her feedback from the judges.
"We love you tom," she wrote in response to Bergeron's post about the incident.
Bergeron had told fans in a tweet Tuesday that he didn't mean to offend Biles with his remark. He admitted his comment to the star was "clumsy."
"Loved @Simone_Biles crisp response to my clumsy question. Curious how she felt about judges comments, I unwittingly added to the smile pile," he said.
Biles and partner Sasha Farber scored a 36 out of 40 on Monday after judges said the gymnast didn't bring enough emotion to her routines. Biles had a short answer for Bergeron after he asked why more positive feedback didn't elicit a smile.
"Smiling doesn't win you gold medals," she responded.
Biles, a four-time Olympic gold medalist, confessed to Entertainment Tonight after her performance that she isn't sure how to win over the judges. She and Farber have yet to receive a perfect score in competition.
"I feel like everyone has their own opinion, clearly, but it's just how you take it," the star said. "I feel like I am trying, I am being honest. If they don't see that, I don't know what else more I can do."