In a two-lap, green-white-checkered-flag dash to the finish, Stewart pulled away from Bowyer, who had inherited second position after a six-car wreck wiped out half the top 10 with three laps left in the regulation distance of 147 laps.
David Reutimann edged Todd Bodine for fourth, and Steve Wallace beat teammate David Stremme for fifth.
Stewart won for the fourth time in six Nationwide starts this year and for the sixth time in his career. It was the eighth Nationwide win in 12 races this season for Joe Gibbs Racing drivers.
"It's this team behind us and this team at Joe Gibbs Racing," Stewart said. "We just took it easy in the beginning and tried to bide our time and take care of the car and take care of the tires and have something for them when we came to the end."
After Mark Martin stalled in the second position on a restart with three laps remaining, triggering a six-car wreck, NASCAR stopped the race for cleanup before Stewart led the field to the green-white-checkered on Lap 148.
With 46 laps left in the race, Matt Kenseth led Stewart by more than two seconds, but Kenseth came to the pits on Lap 121, complaining that his wheels were chattering. The crew changed four tires and sent Kenseth back on the track, but Kenseth wrecked in Turn 4 on Lap 128 trying to catch the first car one lap down.
"They told me the lucky dog was in Turn 1, and I was in Turn 4," Kenseth said. "I was driving way over my head trying to catch him."
Stewart led the field to the restart with 13 laps left and stretched his advantage over Martin to more than one second, but David Ragan spun and pounded the Turn 2 wall on Lap 138 to bring out the seventh caution of the race and set up the restart on Lap 145. That's when Martin's engine sputtered, setting up the green-white-checkered finish.
Polesitter Carl Edwards, who entered the race second in the series standings, chose to start on the outside of Bowyer, the second-place qualifier, but may have regretted that decision after scraping the wall while battling with Bowyer on the opening lap.
On Lap 2, Edwards' race ended prematurely when his No. 60 Ford blew the right front tire and smacked the Turn 3 wall.
"They dropped the green, and I was ready to race," said the defending series champion, who finished 43rd as the first car out. "I got loose and hit the wall. I guess I cut a tire down. . . That was a bad mistake, and I learned my lesson there."
Notes: Part-time Nationwide Series driver Denny Hamlin, who was fastest in the final two practice sessions, slammed into the outside wall during his first qualifying lap Friday and failed to make the race. . . Kyle Busch, who was shuffled back in the running order after a pit stop on Lap 87, lost a chance to take over the points lead from Bowyer when he tangled with Brad Keselowski on Lap 102 and careened into the Turn 1 wall. He finished 31st.
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