The Yellow Jackets gave up 21 second-quarter points, but fought back to take a 26-21 lead on the third scoring run of the game by Tevin Washington with 4:29 left in the third period.
Thomas then drove Virginia Tech 56 yards in nine plays and scored on a 12-yard run to put the Hokies in front for good. He tacked on a 14-yard scoring throw to Chris Drager in the fourth quarter and Cody Journell finished off the scoring with a 23-yard field goal with 3:02 to play.
Virginia Tech improved to 9-1 for the season and is 5-1 in the ACC's Coastal Division. The Hokies have games remaining against North Carolina and Virginia, which will take a 3-2 division record into Saturday's meeting with Duke.
Georgia Tech slipped to 7-3 and 4-3 in the Coastal Division. The Atlantic Division is led by Clemson.
During the second period Thomas scored on a 1-yard run and threw touchdown passes of 9 yards to Jarrett Boykin and 63 yards to Danny Coale. Thomas completed 7-of-13 passes for 209 yards.
David Wilson added 175 rushing yards for the Hokies without scoring a touchdown.