Stewart, who is not qualified to win the Cup, crossed the finish line more than 12 seconds ahead of Casey Mears, who also ran out of fuel on the final lap.
"I just shut (the car) off," Stewart said.
Burton's fifth-place finish earned him a 69-point lead over Denny Hamlin and 70 points over Martin in the championship battle with seven races remaining.
Matt Kenseth, suffering rear end problems, was 28th, Busch finished 29th and was penalized for speeding on pit lane; and Jimmie Johnson finished 14th after being penalized for speeding during his final pit stop.
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