It was Busch's eighth Sprint Cup victory this season. He took the checkered flag by driving his No. 18 JGR Toyota 2.275 seconds ahead of Stewart and became the first Sprint Cup driver to win three road course races in the same season.
"The more we ran, the better this car was," Busch said.
He swept both road-course events in 2008, including the Save Mart 350 at Sonoma, Calif., in June.
Ambrose won Saturday's Zippo 200 Nationwide race, and his third-place finish on Sunday was accomplished despite his last-place start.
The race was marred by a crash involving nine cars with just eight laps remaining. The crash led to the race's fourth caution flag.
Busch leads the Points' standings with 3,254 points. Carl Edwards (3,012) is second and Jimmie Johnson (3,010) is third.