Virginia Tech's defense took it from there.
Thomas shook off a sluggish start to his senior season, Virginia Tech's defense shut down Georgia Tech's proud running game and the Hokies beat the Yellow Jackets 17-10 on Thursday night.
Thomas overcame an abdominal strain to complete 19 of 25 passes for 221 yards and a touchdown and had 16 carries for 58 yards and a touchdown.
"I wasn't sure I was going to be able to make it through," Thomas said. "I wasn't able to practice pretty much all week."
Virginia Tech (4-1, 1-0 Atlantic Coast Conference) earned its fourth straight win over Georgia Tech (3-1, 2-1).
The game often decides the Coastal Division's representative in the ACC championship game. Virginia Tech (five) and Georgia Tech (three) are the only teams from the division to play in the championship game.
Kyle Fuller had two tackles for losses and a forced fumble, Brandon Facyson intercepted a pass and had a forced fumble and fumble recovery and Derrick Hopkins had seven stops to lead a strong performance by the Hokies' defense.
Georgia Tech's fourth-ranked rushing offense was held to 129 yards - more than 200 yards below its average.
"That's something we wanted to do, and we took pride in that," Fuller said.
Georgia Tech coach Paul Johnson said much improvement is needed in his spread-option offense.
"It's been coming," Johnson said about the offense's struggles. "I've told you all along we're not very good with the option. We're terrible, in fact, and it showed. We're not going to throw the ball 24 times and win very many games. That's not us. We've got to be able to run the ball ... and we didn't do it."
Vad Lee completed only 7 of 24 passes for 144 yards with two interceptions while also losing a fumble.
Virginia Tech overcame a short practice week to find a defensive plan to contain Lee and the spread-option offense that was averaging 45.3 points per game.
"I think we're fortunate to have some veterans up front that have played against their offense a couple of times," Virginia Tech coach Frank Beamer said. "It's a rugged offense. You have to be rugged yourself to play it. You have to be very precise."
Led by Hopkins, the 311-pound defensive tackle, Virginia Tech stopped running back David Sims on back-to-back plays, including a fourth-and-2 run, midway through the fourth quarter.
Cody Journell was wide left on a 25-yard field goal for Virginia Tech with 5:37 remaining to keep Georgia Tech's hopes alive. Kendall Fuller intercepted Lee's fourth-down pass from near midfield with 1:06 remaining to clinch the win.
Thomas completed only 48.5 percent of his passes (65 of 134) with six interceptions and only four touchdowns in his first four games. He returned to form against Georgia Tech as he completed his first nine passes.
Georgia Tech trailed 14-3 at halftime before closing the gap with a 14-play drive that consumed more than 8 minutes of the third quarter.
Big plays of the drive were a 40-yard pass from Lee to Robert Godhigh and two Virginia Tech penalties that gave the Yellow Jackets first downs, including a fourth-and-1 offside call on linebacker Jack Tyler. On third down from the Virginia Tech 10, Hokies free safety Detrick Bonner was called for pass interference as he deflected a pass intended for DeAndre Smelter.
David Sims scored on a run from the 2 for Georgia Tech's only touchdown.
Journell's 39-yard field goal pushed the Virginia Tech lead to 17-10.
Fuller moved from cornerback to outside linebacker and Facyson, a freshman, took over at Fuller's cornerback spot.
Fuller, who said the moves were "just specifically for this offense," blitzed on Georgia Tech's first series and reached out to strip the ball from Lee. Facyson recovered at the Georgia Tech 27, and two plays later Thomas threw a 21-yard touchdown pass to D.J. Coles.
Facyson's fourth interception of the season ended Georgia Tech's second possession. Facyson cut in front of Tony Zenon at the Virginia Tech 13 to end Georgia Tech's nine-play drive.
Thomas had a 5-yard touchdown run in the second quarter for a 14-0 lead. Thomas matched Tyrod Taylor's school record of 23 rushing touchdowns by a quarterback.
The Yellow Jackets were called for five false-start penalties in the first half and six overall. Georgia Tech's only points of the first half came on a 49-yard field goal by freshman Harrison Butker midway through the second quarter.
Georgia Tech, celebrating the 100th anniversary of Grant Field at Bobby Dodd Stadium, wore throwback jerseys from the 1950s and 1960s.
Virginia Tech unveiled new silver-blue Hokie Stone helmets and wore maroon jerseys and pants for the first time since playing Miami in 2009.