The defending Sprint Cup series champ started with the poor positioning after his car failed a post-qualifying inspection for using an illegal cooling hose on his Chevrolet.
But using pushing help from teammate Kasey Kahne, he passed Matt Kenseth for the lead on the final lap. Stewart then held Kenseth and Roush Fenway Racing teammate Greg Biffle at bay on the backstretch for his third victory of the year and 47th of his Cup career.
Biffle's car triggered a major wreck on the last lap, allowing Jeff Burton to finish second. Kenseth, meanwhile, settled for a third-place run.
Rounding out the Top 5 were Joey Logano and Ryan Newman.
NASCAR announced before the race that driver A.J. Allmendinger had been "temporarily suspended" for violating its substance abuse policy.