Stewart won his second race of the season and 11th of his career, beating Robby Gordon on the road course at Sears Point Raceway.
With 11 laps to go, leader Robby Gordon was fighting off brushes by Kevin Harvick - who was trying to get back on the lead lap - and missed Stewart's deft pass on Turn 7.
Robby Gordon, subbing for Ultra Motorsports' driver Mike Wallace in a Ford, finished second in the event completed under caution.
Pole-sitter Jeff Gordon was vying for his record-setting seventh road-course victory as well as his fourth straight win at Sears Point. He finished third after leading 32 laps, and remains the Winston Cup points leader.