Harvick and Juan Pablo Montoya -- who was leading at the time -- each pitted during a caution flag in the closing laps after an accident involving Brian Vickers. Jeff Burton, who remained on the track, led at the restart, while Montoya restarted in sixth.
Harvick made his way through the field and finished 0.343 seconds ahead of Bowyer for his 20th career Sprint Cup Series victory, his third at Richmond.
Joey Logano claimed third place while Montoya settled for fourth -- his first Top 10 finish in 30 Sprint Cup races.
Burton finished fifth.