Biffle won the race at Michigan International Speedway, taking advantage of Johnson's troubled engine. An engine change had sent Johnson to the back of race to begin with. He finished 27th.
After Johnson's mishap, there was a caution for oil on the track. Biffle held off Keselowski by 0.416 seconds in the green-white-checkered finish.
Biffle took over the points lead, while Johnson dropped from first to fourth. Matt Kenseth moved up a spot to second despite a 17th-place showing.
"I know that a lot of people don't expect us to win the championship, and don't expect us to compete for the title," Biffle said. "I don't care what they say or who they want to talk about, but we will be a factor when it comes down to Homestead. I promise you that."
Kasey Kahne finished third in the 400-mile race, followed by Dale Earnhardt Jr. and Marcos Ambrose.
It was the 12th victory for Roush Fenway Racing at MIS, breaking a tie with the Wood Brothers for the most wins at the track.
Pole sitter Mark Martin was sailing along in the lead for most of the first 65 laps before his race ended in scary fashion. Bobby Labonte went into a spin while Martin was coming up from behind, and Martin went sliding off toward pit road. His car crashed frighteningly into the end of a short, narrow barrier on the interior side of pit road.
The side of Martin's car was essentially impaled by the end of the wall, just in front of the left rear tire and dangerously close to the driver's seat. But in the smoky scene that followed, Martin was able to get out and walk away.
"I really feel that was a freak accident. I'm not sure you can ever completely fix something like that," Martin said. "That was a pretty freak angle that I got it. I'm not sure what you can do. It could have been really bad if I would have got into that hole a little deeper where it would have caught me in the door instead of the crush area back there."
Johnson did not speak to reporters afterward. He was trying to become the first driver to reach four victories this season.