Bowyer held the lead for 71 of the 112 laps on the 1.99-mile, 12-turn road course and hung on through the green-white-checkered finish for his sixth career win in the Sprint Cup series.
Bowyer is in his first year of driving the No. 15 Toyota for Michael Waltrip Racing.
Defending champion Kurt Busch tried unsuccessfully to take the lead from him in the closing laps, then had to deal with a mechanical problem prior to the two-lap overtime finish.
Matt Kenseth kept his points standings lead despite a 13th-place finish, maintaining an 11-point advantage over Roush Fenway Racing teammate and seventh-place finisher Greg Biffle.