Florida regained the lead 23-20 on Gillislee's 37-yard run with 11:01 left in the final period on the first play after Florida State's E.J. Manuel fumbled, his fourth turnover of the game. Gillislee finished with 140 yards rushing.
Florida (11-1, 7-1 Southeastern Conference) came into the game fourth in the BCS standings, and the gators could find themselves in position to earn a spot in the national championship game if No. 1 Notre Dame loses to Southern California. The Gators lone loss was in late October to third-ranked Georgia, and it will keep them out of the SEC title game.
Florida State (10-2, 7-1 Atlantic Coast Conference) was hurt by five turnovers in the game. The Seminoles will play Georgia Tech next week in the ACC title game.
Florida State was hoping to keep its own long shot national title hopes alive, and restore a bit of respect for its conference, with a third straight win over the Gators, but couldn't.
Florida salted its victory away on a Jeff Driskel's 14-yard touchdown throw to Quinton Dunbar with seven minutes left and Matt Jones' 32-yard run with 2:33 left for a 37-20 lead.
Caleb Sturgis kicked three field goals for the Gators. Florida State's Dustin Hopkins had field goals of 50 and 53 yards to tie former Georgia kicker Billy Bennett's NCAA record of 87 career field goals.
Florida State scored 20 straight points to wipe out an early 13-0 deficit. Manuel threw a 6-yard TD pass to Nick O'Leary and the quarterback bootlegged in from a yard out with 8:30 remaining. When Dustin Hopkins kicked a 53-yard field goal with 4:24 left in the third, the Seminoles looked as if they were on their way.
But Florida dominated the fourth quarter.
Gillislee's go-ahead TD run came the first play after Florida's Dominque Easley recovered the fumble by Manuel, who coughed up the ball after being nailed by Antonio Morrison. Manuel had to leave the game for a series, but was unable to rally the Seminoles after returning to the game.
It was a tough game for Manuel for the second straight year against the Gators. He threw for only 65 yards in a 21-7 win at Florida last season and was intercepted three times Saturday in addition to the costly fourth quarter fumble. It was only the second time he was intercepted three times in a game.
Florida dominated the first half, building a 13-0 lead before Florida State scored on the final play of the half when Dustin Hopkins kicked a 50-yard field goal into the wind.
Sturgis hit field goals of 39 and 45 yards and Gillislee scored on a 9-yard run moments after the Gators recovered a fumble on the kickoff by Florida State's Karlos Williams at the Seminoles 21.
The Gators, who missed a golden scoring opportunity near the end of the first quarter when Trey Burton underthrew a wide open Clay Burton at about the Florida State 10, ran 25 plays in The Opening quarter to eight for the Seminoles.
Florida also had a chance to add to its 13-0 lead after intercepting Manuel the second time in the half at Florida State's 24.
However, Jeff Driskel was sacked for a 10-yard loss after a false start penalty that pushed the Gators too far back for another field goal try by the steady Sturgis.
After two running plays drew boos from the home crowd, the Seminoles took to the air in the final 39 seconds and Manuel found Kenny Shaw twice for 27 yards on a short drive to set up Hopkins 50-yard field goal as time expired in the half.