Jeff Gordon of Hendrick Motorsports finished in second, with Roush Fenway Racing's Greg Biffle in third.
Earnhardt kept it until his other teammate Jimmie Johnson emerged in the first position after the first round of green flag pit stops took place.
Because of Stewart's victory, Chevrolet won its 33rd Manufacturers' Championship in NASCAR Cup Competition, as Toyota could not catch its points total with seven races left in the season.
[6] Before the race, Mark Martin led the Drivers' Championship with 5,400 points, and Jimmie Johnson stood in second with 5,390.
Tony Stewart, Martin Truex Jr., A. J. Allmendinger, David Stremme and Brad Keselowski rounded out the session's top ten fastest drivers.
[2] Hendrick Motorsports and Chevrolet took the first three places as Martin clinched his seventh pole position of the season, his first at Kansas Speedway, and the 48th of his career, with a time of 30.724 seconds.
He was joined on the grid's front row by his teammate Dale Earnhardt Jr. whose best lap was 0.084 seconds slower.
Kahne, Joe Nemechek, Bowyer, Gordon and Scott Speed completed the top ten positions.
Gordon managed sixth, Vickers was seventh fastest, Logano eighth, McMurray ninth, and Edwards tenth.
Country music singer Blaine Larsen performed the national anthem, and the Grand Marshal of the race Kent Blair commanded the drivers to start their engines.
[19] On lap two, Logano lost control of his car, and spun sideways off the track at turn two, causing the first caution.
One lap later, the second caution was prompted after Paul Menard spun sideways at turn two, collecting Ragan, Michael Waltrip, Max Papis, and Bobby Labonte.
On the 21st lap, Johnson claimed the sixth position from Kahne, while Montoya passed Gordon for eighth.
[19] On lap 48, Montoya was overtaken by Biffle for the eighth position, and Reuitmann got ahead of Martin on the outside lane to take fifth on the backstretch.
[1] Kenseth was passed by Montoya for second on lap 76, and Keselowski and Kurt Busch battled for fourth place.
[21] Johnson drew ahead of Biffle as the pair crossed the start/finish line to lead the 91st lap, as Stewart got past Truex for the third position.
Johnson and Biffle continued to trade the lead for the next three laps, as they extended their advantage over the rest of the pack to five seconds.
Biffle was delayed the slower car of Papis, and Johnson took the opportunity to get ahead of him, and retake the lead on the 102nd lap.
The second round of green flag pit stops for tires and car adjustments got underway on lap 122.
Elliott Sadler pirouetted through 360 degrees in turn two, but avoided contact with the wall and passing vehicles on lap 147, activating the fifth caution.
[21] Three laps later, Gordon passed Martin for fourth, and Marcos Ambrose lost the tenth position to Kahne.
The third phase of green flag pit stops for fuel, tires, and car adjustments occurred between laps 183 and 209, with Biffle maintaining the lead and Stewart keeping second.
[19] On lap 212, Montoya's crew chief Brian Pattie requested he conserve fuel so he could try to finish the race.
During the caution, the leaders (including Biffle), elected to make pit stops for fuel and tires.
[1] He credited his crew chief Darian Grubb for a strategy that allowed him to take the lead, "The guys that took four could just never gain the track position back.
"[23] Third-placed Johnson said of his situation in the championship and the loss of a victory, "I hate losing points, I felt like we had a shot to win the race, it's just way too early, for myself, even to start worrying about [the Chase standings.]
"[25] Although he finished seventh, Martin said he was pleased with the result as he was able to keep the points lead, "This is the first time we missed it that much in a while.
"[27] After the race, Johnson's and Martin's cars were transported to NASCAR's Research and Development Center in Concord, North Carolina for a further precautionary inspection because those two vehicles had been close to exceeding to the organizing body's measurement tolerance limits at the previous week's race at Dover International Speedway.
Hamlin, Gordon, Biffle, Newman, Edwards, Kahne, and Vickers completed the top twelve drivers in the points standings.
[30] Because of Stewart's victory, Chevrolet won its seventh Manufacturers' Championship in a row, and its 33rd in NASCAR Cup Series competition.