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Thomas did not accompany the Gators on their trip to Vanderbilt.
"Marcus did not meet his responsibilities and obligations to remain on the team," coach Urban Meyer said in the statement.
After Florida beat Vanderbilt 25-19, Meyer was asked about Thomas. He repeatedly referred reporters to the statement.
Defensive coordinator Charlie Strong said the Gators were made aware of the decision and why the move was made Friday.
"You hate to lose any player. What happened is you just feel bad because you look at the talent he has, not just the talent, you look at the relationship he had with the players," Strong said. "And they do understand."
Thomas, one of Florida's best defensive players, served a two-game suspension following a failed drug test earlier this year. He was reinstated in October and played against LSU, Auburn and Georgia.
A 6-foot-3, 296-pound senior, Thomas had 26 tackles, including four sacks, in five games.
ESPN college football reporter Joe Schad and The Associated Press contributed to this report.