The five-time defending champion was running seventh with 17 laps remaining when contact with Ryan Newman sent him headfirst into the wall. The hit was so hard, his back tires briefly lifted off the track.
He finished 34th and dropped to eighth in the Chase for the Sprint Cup standings with five races remaining.
Johnson, winner of last week's race at Kansas, had started the race ranked third in points and only four points behind leader Carl Edwards.
"That one stung for sure. Pretty big impact," Johnson said. "Definitely not the night we wanted. This is not going to help us win a sixth championship."
Johnson was on the cover of Sports Illustrated this week, and had dismissed the idea of falling prey to the so-called cover jinx.
After notching his lowest Chase-race finish since he was 38th at Texas in 2009, he may now be wondering if the curse is credible.
"What happened to Jimmie Johnson is a sobering lesson for everyone," winning car owner Jack Roush said.
Kenseth, meanwhile, was celebrating in Victory Lane for the third time this season.
He quietly hung near the front all night, but missed several chances to take the lead because of botched restarts. He finally got it right with 25 laps remaining when he sailed past Busch, and held him off again on the final restart with 13 laps to go.
The victory moved Kenseth up two spots in the standings to third, only seven points behind Edwards at the halfway point of the Chase.
"It was tough to get by him and I am glad we could make it by him because it was challenging," Kenseth said. "I was going to be pretty mad if I was going to lose this thing on restarts. Finally got one on the end."
Busch, who led a race-high 111 laps, settled for second. Although it was his best finish of the Chase, he was frustrated to fall short of the victory.
He also had a late run-in with Edwards, who finished third and leaned into Busch's car after the race to discuss an incident in the closing laps.
They two seemed fine with each other after the talk, with Busch insisting he did not race dirty and Edwards apparently accepting his explanation.
"There was no malicious intent involved," Busch said. "It was just a product of what we had at the end, giving everything we had and trying to come home second."
Busch probably had the best night of anyone after an engine change forced him to start last in the 43-car field.
Despite early frustrations with the handling on his Toyota, he drove to the front and was in command until Kenseth came on strong.
"Just got outdrove," Busch said. "He just flat drove past me."
Kasey Kahne and Marcos Ambrose, two drivers not competing for the championship, finished fourth and fifth. It was the third straight top-10 finish for Ambrose, the first time in his career he's pulled that off.
Kevin Harvick was sixth, and he went from one point behind Edwards to fourth. AJ Allmendinger was seventh and was followed by pole-sitter Tony Stewart, who overcame late contact with Greg Biffle to finish eighth.
Denny Hamlin was ninth and Ryan Newman rounded out the top 10.