The victory was the third for Stewart in the first seven races of the 10-race playoffs, and he was easily the leading benefactor as the points race was significantly jumbled.
Stewart moved from 19 points behind leader Carl Edwards and in fourth place to just eight points behind in second as several contenders got caught up in a season-high 18 caution flags.
"He better be worried. That's all I've got to say," Stewart said in Victory Lane.
Edwards struggled all day, twice needing to get a free pass as the first car a lap down. He made it pay off the second time, rallying to finish an unlikely ninth.
"That's just a gift," he said. "We did not deserve to finish ninth."
Others deserved much better than what they got, namely Matt Kenseth and Brad Keselowski. They started the day second and third in points, and both were running near the front all day until getting caught up in late accidents. Kenseth finished 31st and Keselowski wound up 17th.
It seemed especially harsh for Kenseth, who was doing uncharacteristically well for him on the 0.526-mile oval until tangling with Kyle Busch on lap 464. Kenseth wound up in the garage.
"That ruined my day, along with his and whoever else got unfortunately collected in that mess," Kenseth said about Busch, who also ran up front all day but limped home in 27th place.
"That was crazy. The racing was crazy," Jeff Gordon said after finishing third, followed by Kevin Harvick, Denny Hamlin, Jeff Burton, Dale Earnhardt Jr., Martin Truex Jr. and Edwards.
Johnson, who started the day seventh in points, moved into sixth with his second-place run, but is still 43 points off the lead in search of his sixth consecutive championship.
Harvick moved into third in the points race — 21 behind Edwards heading to Texas.