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Burton passed Hamlin before the 11th and final caution came with 26 laps remaining. Prior to the caution, Gordon was attempting to make his final pit stop of the race but was blocked by Tony Stewart and missed the entrance to the pits. Gordon fell back to the last car on the lead lap.
During the caution, Hamlin took only two tires and exited the pits first. Burton had to serve a pass-through penalty after running over his air hose while leaving his pit stall.
Hamlin finished nearly two seconds ahead of pole sitter Jamie McMurray for his third win in the last six Sprint Cup races.
Kurt Busch was third, while Gordon rallied in the closing laps for the fourth position. Juan Pablo Montoya completed the top-five. Burton wound up eighth.
Jimmie Johnson finished 36th after he was involved in an accident with A.J. Allmendinger just before the halfway point in the 501-mile race. Kevin Harvick's sixth-place finish allowed him to take a season-high 110-point lead over Johnson.
1. Denny Hamlin, Toyota
2. Jamie McMurray, Chevrolet
3. Kurt Busch, Dodge
4. Jeff Gordon, Chevrolet
5. Juan Pablo Montoya, Chevrolet
6. Kevin Harvick, Chevrolet
7. Kyle Busch, Toyota
8. Jeff Burton, Chevrolet
9. Ryan Newman, Chevrolet
10. Brian Vickers, Toyota
Complete Showtime Southern 500 Results Here