Gordon rebounded after falling off the lead lap early in the race and to 25th when the race was stopped by rain.
"Man, that was an awesome effort," Gordon said. "I'm just so fired up to get this Chase started, I don't care we're going to start in points. We're in it."
Mark Martin finished third, followed by Tony Stewart and Matt Kenseth.
Denny Hamlin led the most laps but placed 18th. He still clinched the top seed in the Chase with four victories.
Busch finished 16th and missed the Chase by three points on a wild-card tiebreaker to Gordon.
"We missed," said Busch, who had a slow final pit stop. "Plain and simple."
Asked what team owner Joe Gibbs told him immediately after the race, Busch said, "Handle it the right way. There's no right way to handle this situation."
The pivotal moment came on a lap 277 caution for rain. Busch was among several drivers who didn't pit immediately, gambling the rain might stop the race. When it didn't, he had to pit and lost several spots.
"We missed it," crew chief Dave Rogers radioed his driver afterward. "My fault. 100(PERCENT) my fault. I blew it."
Hamlin was equally deflated after having the night's dominant car and seeing his Joe Gibbs Racing teammate miss the Chase.
"It's a tough day all around for JGR," Hamlin said.
Hamlin started seventh and took his first lead on lap 59. He led 85 of the next 94 laps (yielding briefly to pole-sitter Dale Earnhardt Jr., who led 69 laps) before the race was stopped for a rain shower.
After a 52-minute red flag, the race was restarted on lap 153 and went green again three laps later with 245 laps remaining.
During a competition caution on lap 47, Gordon dropped to 19th as his crew completed major adjustments to help the handling of his Impala.
But the changes didn't seem to improve the car, and the four-time champion began struggling with his brakes while falling outside the top 20. He went a lap down on lap 128 and was in 25th when the race was red-flagged for rain on lap 152.