Johnson stretched his record run of championships to a five straight by making the fewest mistakes in Sunday's season finale.
Johnson trailed Denny Hamlin by 15 points entering Homestead-Miami Speedway, but captured another title by running the cleanest race of the three championship contenders. He finished second to race winner Carl Edwards and claimed the championship by 39 points over Hamlin.
Kevin Harvick finished third in the race, and third in the final standings, 41 points behind Johnson.
"I was after it pretty hard," Johnson said. "Even if you aren't a 48 fan, I think you saw something special today."
It was the first come-from-behind championship in the seven years of the Chase for the Sprint Cup championship format, which debuted in 2004 and was won each year by the driver who took the points lead into the finale.
That wasn't Johnson this year. Not even close.
Hamlin, with a series best eight wins this season, was the best as the season came to a close. But poor fuel mileage last week in Phoenix kept it tight headed into Sunday, and he had a terrible race when he needed only a clean run.
Contact with Greg Biffle very early in the race sent Hamlin into a spin and damaged the front of his car. He dropped to 37th by the restart and had to work all day to finish 14th.
"We had a great year, we won the most races that we ever won, we contended like we've never contended before and just circumstances took us out of this one," Hamlin said.
Harvick, meanwhile, took the lead on a round of pit stops with 80 laps to go, but was flagged for speeding as he entered pit road. It dropped him to 29th, and he was still upset with the call after the race.
"I don't think that penalty will ever settle in my stomach," Harvick said, insisting that "only a handful of people" get to see the pit road speeds. "I won't ever settle for that."
But he wasn't devastated by the defeat, pointing to all the gains made this year by Richard Childress Racing. A year after failing to put any cars into the Chase, RCR had three in the field and Harvick, winner of two races, led the points for most of the regular season.
"It's a 180 for us," Harvick said. "Last year this time we all wanted to put a gun in our mouth."
While Harvick could find the bright spots, Hamlin, sitting next to him at the podium, had a harder time finding much to be happy about. With a vacant look and muffled answers, he vowed to be back stronger next season.
"My job is to work in the offseason to do everything I can to be better and, you know, I know every year that I am in the Cup series, I'm going to be better than I was the previous year," Hamlin said. "We're going to keep working and go get them next year."
As both drivers discussed their day, Johnson's championship celebration was shown on the multiple televisions hanging around the room and both drivers watched portions of the presentation.
Who could blame them? It was history.
The fifth title moved Johnson past Hendrick Motorsports teammate Jeff Gordon for most titles among active drivers. He now ranks third on the career list behind seven-time champions and Hall of Famers Richard Petty and Dale Earnhardt.
"Finally, finally, after being able to pull this off, he'll get the respect and the rewards that he deserves," crew chief Chad Knaus said.