Keselowski dominated Saturday night at Charlotte Motor Speedway but ran out of gas with 58 laps remaining to blow his chance at the victory.
He fell a lap down and finished 11th, and had his lead in the standings sliced in half.
Keselowski has a seven-point lead over five-time NASCAR champion Jimmie Johnson at the halfway point of the Chase.
Denny Hamlin finished second and is third in the Chase, 15 points back. Johnson finished third.
Everyone had to race with one eye on the gas gauge, and it worked out in Bowyer’s favor for his third victory of the season.
Meanwhile, Dale Earnhardt Jr.’s replacement made an early exit.
Regan Smith, filling in for the concussed Earnhardt for at least two races, went to the garage with a blown engine early in the race.
Smith was running extremely well early having moved up from 26th to 10th before smoke began borrowing from his car.
He said he wasn’t sure exactly what went wrong with the car, but immediately parked it behind the wall for the night.
“It’s disappointing and it’s a shame,” Smith said.
Smith also will drive Earnhardt’s No. 88 Chevrolet next week at Kansas.
Matt Kenseth couldn’t carry over his momentum from last week’s win at Talladega, spinning out and hitting the wall after his left rear tire went down minutes into the race.
Although Kenseth was able to continue, he fell a lap down.