Thomas (3-5) drove to the Fairport 40 yard line but a Hail Mary pass fell to the ground in the end zone amid traffic and the Raiders (6-2) held on.
Fairport will play No. 2 Rush-Henrietta in the semifinals on Sunday, Oct. 30.
Joe Oca broke a 7-7 halftime tie with a two yard TD run that gave Thomas the lead early in the third quarter.
Vaughn responded late in the 3rd with a three yard quarterback sneak to tie things at 14.
The turning point of the game may have come early in the 4th quarter. Thomas had first and goal at the Fairport five, but ended up going backwards four yards in four plays and turned the ball over on downs.
Two plays later, the Red Raiders fumbled the ball right back at the Fairport 25. However, Thomas again could not find the end zone and settled for a 20-yard field goal and a 17-14 lead. That set the stage for Fairport's game winning drive.