The 500-mile race ended under a caution flag after a major crash on the final lap that saw A.J. Allmendinger's car go airborne and flip upside down before rolling back over.
Bowyer got credit for his second Chase victory this season, edging Richard Childress Racing teammate Kevin Harvick, after race officials finished their reviews. Bowyer also won the first race in the playoffs last month at New Hampshire.
Harvick was given second place in a race that featured 87 lead changes, one short of the all-time NASCAR record set at Talladega earlier this year.
Jimmie Johnson ended up in seventh place, taking a 14-point lead over Denny Hamlin in the Sprint Cup standings. Hamlin finished ninth.