Thompson was hurt after a juggling 32-yard catch, when his knee bent awkwardly while being tackled. He was helped off the field, and the school announced later he was out.
At the time of his injury, Thompson had 94 of the Seminoles' 112 total yards.
The senior is a leading candidate to become the ACC's comeback player of the year after missing most of last season with a broken back. He returned this season and came into Saturday's game with 640 total yards, putting him on pace to become the school's first 1,000-yard rusher since Warrick Dunn in 1996.
Without him, Florida State will rely on James Wilder Jr. and Devonta Freeman. Wilder ran for a touchdown on the drive in which Thompson got hurt.