Busch thought he mapped out the strategy to take him to Victory Lane.
Instead, he ended the race in the infield care center after a vicious last-lap accident sent him flying into the wall as Stewart skirted by for a somber win.
"That's not the way I wanted to do it," Stewart said after his Saturday night win gave him his third victory in five years in Daytona's summer race.
Stewart had the dominant car, leading a race-high 86 laps and using a flawless pit-road performance to set himself up for his second win as owner of his race team. But Busch had other ideas, taking the lead seconds before the last lap to start a frantic 2.5-mile chase between the former teammates.
Busch passed Stewart right before the final lap to take the lead, but Stewart chased him down and calculated his next move. Stewart closed in on Busch's bumper, and slight contact sent Busch drifting up the track.
Busch slid back down to maintain his lead, then tried to slide in front of Stewart to block Stewart's next move. The cars were too close together and Stewart hooked Busch's right corner to send Busch sailing into the wall.
Stewart celebrated his 35th career Sprint Cup victory with a bit of heartache.
Busch left the speedway with a definite headache.
"I just don't like it to end that way," Stewart said. "You know, you work hard to get to this level and you don't want to see races decided by guys wrecking coming to the finish line. That's not what it's about. Maybe I am being hard on myself, I don't know. But I just don't like the way that ended up."
Just another wild restrictor-plate finish for NASCAR, which is still smarting from a frightening crash in April at Talladega Superspeedway, where Carl Edwards went airborne into the fence in a similar last-lap crash.
Stewart usually takes every win any way he can. But after wrecking Busch in the frantic finish, he wasn't in the mood to gloat.
"I am not shaken by it, it doesn't matter who it is, you don't want a race to be decided like that," Stewart said. "It's just a bad situation. I don't feel as much gratification for winning the race as I should."
The contact triggered a multiple-car crash behind them, but Stewart sailed through for his second points win of the season. The two-time series champion is leading the points in his first season as co-owner of Stewart-Haas Racing, which he overhauled from a backmarker team into a title contender after 10 seasons at Joe Gibbs Racing.
"I went where I had to go, and he went where he had to go," Stewart said. "You hate seeing a guy that's been up front all day, especially a guy that's helped me the whole race, wreck like that. You're kind of forced in that position. But I made my move to the outside and he went to block us and we were already there.
"It still doesn't mean you like it. That's not the way to win these things. If I did something wrong, I'm sorry."
It was a horrendous wreck for Busch, who climbed from his car apparently unscathed but had to be forced by four NASCAR officials into a waiting safety vehicle. He finished 14th and refused to comment after the race.
Team owner Joe Gibbs briefly checked on Busch, who needed intravenous fluids after driving a 70-minute stint in stifling heat earlier Saturday in his Grand-Am Series debut. Gibbs said Busch had a headache, and would be monitored overnight for precautionary reasons.
"It's a tough place to race," Gibbs said. "I felt like he gave it everything he could. I'm proud of him."
Marcos Ambrose was sixth, followed by Brian Vickers, who came back from an accident, and Daytona 500 winner Matt Kenseth. Juan Pablo Montoya rallied from a lap down to finish ninth, and Elliott Sadler rounded out the top 10.
But post-race was subdued as the competitors contemplated the dangers of restrictor plate races. NASCAR uses the horsepower-sapping carburetor plates to slow the speeds at Daytona and Talladega, the two fastest tracks in the series.
It causes the cars to run in tight packs, where one small wiggle can trigger a multiple-car accident. This race was plagued with an earlier 13-car wreck that collected several contenders for the Chase for the championship, and the last-lap accident in which Busch's car lifted slightly off the track as it went nose first into the wall.
"It's plate racing. We're damned if we do, damned if we don't," Johnson said. "The guys are racing. Tony didn't mean to dump him. It's just the product of restrictor-plate racing. Every time we leave these restrictor-plate tracks, there's questions about how we can keep from having the big wreck and things like that.
"You just can't."