Thomas is a former five-star recruit from Miami, but injuries and suspensions have cost him most of his first two college seasons. The sophomore was still recovering from a spring shoulder injury and was already expected to miss about half this season.
Coach Jimbo Fisher said after practice Wednesday that Thomas was ineligible, but did not specify why.
A shoulder injury forced Thomas to redshirt as a freshman. He missed the first six games last season because of an NCAA suspension. He played the final eight games and finished with 26 tackles.
Linebacker Lorenzo Phillips, a junior college transfer, was cleared to play and practiced with the team for the first time Wednesday.