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.