It was the 24-year-old Busch's fourth victory this season -- one more than Stewart and one behind fellow young gun Matt Kenseth for the circuit lead -- and his third in the last five races.
Busch, who started on the pole, passed rookie Ryan Newman for the lead with 11 laps to go inside the second turn. He kept the Roush Racing Ford Taurus in front for the remainder of the event.
Stewart survived a raucous weekend on and off the track to finish 18th. Mark Martin, his nearest pursuer in the points race, finished fourth to give Stewart a 38-point edge at the end of the season -- slightly more than a point per race.
Stewart also has won titles in the United States Auto Club in 1995 and the Indy Racing League in 1997.
"This car liked clean air, but it didn't like being in the back of the pack," Stewart said. "We got the spots we needed to finish ahead of Mark Martin in the standings. But it's my crew chief who deserves all the credit for this."
"We gave it everything we had," Martin said. "Those guys were just stronger than us all year. I only regret that I wasn't stronger and couldn't have given these guys another 100 points or so. But I didn't and I'm still proud of what we were able to do this year."
"There are a lot of people in this championship for us that didn't get to celebrate the other one," Gibbs said.
Stewart was congratulated by fellow driver Dale Jarrett and hugged crew chief Greg Zipadelli on the championship platform.
"Zippy made some changes, we got out there, got our lap back and made it back on the lead lap," Stewart said. "It made the last 31 laps a little easier, but it wasn't a piece of cake by any means."
"We've had a tough year," Zipadelli said. "We had some ups and downs, but we were able to do it."
Martin's appeal of a 25-point penalty for an illegal coil spring was denied Saturday, making Sunday's task doubly difficult. He finished second in the standings for the fourth time in his career and has never won the season-long points race.
"I never really looked at this thing this year and allowed myself to think that I would win it and that's a good thing because I feel no letdown now," Martin said. "But I had so many people that wanted me to win this so bad, I started to get nervous that it meant I let them down."
"This is unbelievable," Busch said. "We had to go for the victory. There was no way they could get by us. To have a car that was so good for the pole and then so good for the race. This is an awesome year. We can't wait for next year."
Busch finished third in the standings, 159 points behind Stewart.