The two-time champion saw the coin flip after running out of fuel on the last lap while leading the same race last year, handing victory to his Richard Childress Racing rival. This time Bowyer was up front following the final round of pitstops, but he failed to make it to the end, running out of gas while leading with two laps remaining.
Stewart was there to pick up the victory on a day when his team had yet another good display, his team-mate Ryan Newman leading the race early on from pole position, although having to pit for fuel a few laps from the end cost Newman a top 10 finish.
Once again Stewart had to recover ground to start with, having qualified only 20th while his team-mate set the pace on a flying lap on Friday. Stewart was able to make good progress and was a top-10 contender for most of the second half of the race, his team making the right strategy calls that put him in contention for victory.
Although not the first time a driver has won the first two Chase races - Greg Biffle did it in 2008 - Stewart continues to make a strong claim for the championship as most of the favourites have not been able to get their title bids off to good starts.
"It's way too early to be counting chickens right now," said Stewart after his 41st career win, his eighth ever in a play-off race.
"The closer we got to the front, the better our car drove. We may not have been the best car at the end, Clint was just a tick better than us. I definitely did not know he was in this situation having to worry about fuel.
"The good thing is [crew chief] Darian Grubb told us we were two or three laps to the good [on fuel mileage] and I just got to run hard all the way to the end... We weren't the fastest car, but we were solid and could maintain that pace the whole last 100 laps."
Penske's Brad Keselowski finished second after struggling early on, picking up the runner-up spot from Roush Fenway's Biffle, who ran out of fuel on the last lap. Keselowski's solid finish allows him to keep his pre-Chase momentum and move up to third in the standings.
Biffle was the best of the Roush Fenway drivers in third ahead of Hendrick Motorsports' Jeff Gordon, who led the most laps after getting a lucky break during the second caution of the day, when he caught most of the field a lap down as he led while delaying his pitstop.
However Gordon had to surrender his victory hopes when he was informed that not enough fuel had gone inside the tank of his car after the last stop, although he still came home a strong fourth, which vaults him up six spots in the Chase ranking after running out of fuel last Monday at Chicagoland.
Red Bull's Brian Vickers rounded out the top five on a good day for his outfit, his team-mate Kasey Kahne leading for 42 laps but having to pit once more than the leaders 16 laps from the end while running inside the top five.
Roush's Matt Kenseth recovered from a spin after being tapped by team-mate Carl Edwards, the pair finishing sixth and eighth respectively split by the fellow Roush car of David Ragan. Earnhardt Ganassi's Juan Pablo Montoya had a solid day after a good strategy call allowed him to break inside the top 10, where he raced for most of the day.
Kyle Busch finished 11th after a late clash with reigning champion Jimmie Johnson, the pair making contact a couple of times at Turn 1 but the Hendrick driver suffering most, with suspected damage to his car's right side, which placed him down in 18th in the end. Johnson has dropped to 10th in the Chase, his worst ever position in the play-off ranking.
Former Chase leader Kevin Harvick was 12th but never a threat for victory. He rued his fuel mileage relative to his team-mate Bowyer over the radio in the closing laps but he eventually managed to make it to the end and lost only one spot in the play-off standings.
Hendrick Motorsport's troubled day was compounded by right-front flat tyres for Dale Earnhardt Jr and Mark Martin in the second half of the race, the latter after leading 46 laps and looking set for a strong finish.
Penske's Kurt Busch managed just a 22nd place, following a delay in pre-race inspection that had his car arrive on the grid at the last minute. He struggled for balance for most of the day and crossed the finish line a lap down, losing ground in the title battle.
Denny Hamlin's title hopes are all but over now as the Joe Gibbs Racing driver ran out of fuel with three laps to go, taking a 29th-place finish that keeps him at the bottom of the Chase ranking and 66 points off Stewart.
