The five-time champion goes to next Sunday's season finale at Homestead needing to finish 23rd or better to win the title.
Kenseth, who won his only championship 10 years ago, gave what sounded like a concession speech following his disappointing day.
"Of course I'm disappointed we go there basically without a shot to win," Kenseth said. "On the other hand, I couldn't be happier and more proud of my team and, man, this has been the best year of my racing career. "
Johnson, who had a mechanical failure in last year's season finale and finished 36th, wasn't ready to claim the title following his workmanlike performance at Phoenix.
"We're heading into Homestead in the position we want to be in," Johnson said. "I'll have to go down there and run 400 miles. It's far from over.
Harvick won at Phoenix for the second consecutive year, capitalizing when Carl Edwards ran out of gas coming to the white flag. But all eyes were on Kenseth, who struggled mightily for the first time in the Chase for the Sprint Cup championship and for one of the few times this season. Kenseth had only finished lower than 23rd four times this entire season, and three were related to either engine failure or a crash.
But his car was off from the very start, and he struggled to even tell crew chief Jason Ratcliff what adjustments to make on a Toyota he described at one point as "just not drivable."
"I don't even know what to tell you to fix, to be honest," Kenseth radioed. "I am so aero tight. So aero tight."
Figuring track position and clean air was the only fix, Ratcliff opted for a strategy of having Kenseth do the opposite of other drivers: If they pitted, Kenseth did not, and vice versa. It worked as Kenseth cracked the top 10, but then backfired badly on a pit stop at the worst possible time.
The Joe Gibbs Racing crew botched the pit stop, changing strategy mid-stop, and Kenseth compounded the problem by running over his air hose. His car had to be backed up before it could be serviced. It dropped him to 30th, two laps down, and he restarted behind Johnson at the one opportunity he'd had to make up some ground.
1. Jimmie Johnson
2. Matt Kenseth -28
3. Kevin Harvick -34
4. Kyle Busch -57
5. D. Earnhardt Jr. -63
6. J. Gordon -80
7. Greg Biffle -83
8. Clint Bowyer -87
9. Joey Logano -97
10. Kurt Busch -99
11. Ryan Newman -125
12. Kasey Kahne -132
13. Carl Edwards -134