Shaw had 230 yards passing on nine completions, all to Thomas, Dwyer ran for a career-best 159 yards and Georgia Tech shut out Duke 27-0 on Saturday.
Shaw had a 2-yard touchdown run on the first play of the fourth quarter and completed an 88-yard touchdown pass to Thomas later in the period.
Shaw, a freshman, made his first start as Josh Nesbitt was held out with a hamstring injury. Shaw, sticking with Thomas, finished 9-for-13 with a touchdown.
The 230 yards receiving by Thomas is the second-highest total in school history; Dez White had 243 yards against Virginia in 1998. The 88-yard touchdown reception is the third-longest in school history.
Georgia Tech (4-1 overall, 2-1 Atlantic Coast Conference) led only 3-0 before Roddy Jones' 4-yard touchdown run in the third quarter.
Duke (3-2 overall, 1-1 ACC) suffered its 17th straight ACC road loss, one week after winning at home against Virginia to end a streak of 25 straight conference losses overall.
Duke, which averaged 30.8 points in its first four games, was shut out for the first time since a 13-0 loss to Richmond to open the 2006 season.
Duke was held to 132 yards, the third-fewest allowed by Georgia Tech in an ACC game.
The Blue Devils' deepest penetration in the first three quarters was the Georgia Tech 46 late in the first quarter. Duke began a fourth-quarter drive at the Georgia Tech 47, but it was pushed back 2 yards.
Duke was stopped on a fourth-down play at the Georgia Tech 21 late in the fourth quarter.
Thaddeus Lewis finished 15-for-28 for 97 yards with an interception for Duke.
Dwyer had long runs of 25 and 10 yards as Shaw opened with a 12-play drive. But on second down from the Duke 8, Shaw fumbled when trying to hand off to Dwyer, and defensive end Wesley Oglesby recovered for the Blue Devils at the 9.
Georgia Tech held the ball for an 11-play drive that ended when Clifford Respress grabbed Shaw by his jersey and finally pulled the quarterback down on a fourth-down play at the Duke 29.
A 32-yard pass from Shaw to Thomas helped set up a 20-yard field goal by Scott Blair in the second quarter. A review confirmed Thomas caught the pass before fumbling out of bounds.
Georgia Tech, leading 3-0, let Dwyer do most of the work in its first touchdown drive. Dwyer had four runs for 51 yards on the final four plays of the third quarter, setting up Shaw's 2-yard touchdown run on the first play of the fourth quarter.