Johnson entered the race at Homestead-Miami Speedway with a 28-point advantage over Matt Kenseth, and was among the leaders for much of the event before nearly wrecking after a bump with Kenseth.
He fought back from 23rd place to ninth, ending the season 19 points ahead of Kenseth, who finished second to Denny Hamlin in Sunday's race.
Kevin Harvick also had a shot at the Sprint Cup tile, but finished 10th, ending up 34 points behind Johnson.
Hamlin, meanwhile, took his first victory of the season.
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