A spokesman for Stewart said the 42-year-old driver broke his right tibia and fibula and had surgery after he was transported to a local hospital. An update was expected Tuesday afternoon, and Stewart-Haas Racing did not immediately announce a replacement driver for Stewart's No. 14 Chevrolet at Watkins Glen, where Stewart is a five-time winner.
The team did cancel its scheduled Tuesday test at Atlanta Motor Speedway.
The sprint car accident came a day after Stewart finished ninth in the NASCAR race at Pocono Raceway. He's 11th in the Sprint Cup standings with five races to go until the Chase for the championship field is set.
Stewart was leading the 30-lap feature in a 360 winged sprint car with five laps remaining when a lapped car spun in the fourth turn and collected Stewart and two others.
Race winner Brian Brown told the Des Moines Register he saw the accident in front of him, turned left, hit an infield tire and kept going.
"It looked like he got into a lapped car," Brown told The Register. "When I got close, he was flipping cage down. I didn't really have time to watch and see what was going on.
"First and foremost, we're concerned about Tony and making sure he's all right. He's a huge asset to our sport, especially sprint car racing and an icon in the whole motorsports field. Any time you see him wreck like that and then leave in an ambulance, it's never good. Hopefully he's OK. We weren't going to win that race. We were probably going to run third or fourth."
NASCAR Nationwide Series regular Kyle Larson finished second, telling The Register he ducked through the infield to miss the wreck.
It's the third time Stewart has wrecked in the past month while competing in extracurricular races.
Stewart took responsibility for triggering a roughly 10-car accident at Canandaigua (N.Y.) Motorsports Park on July 16 in which 19-year-old Alysha Ruggles suffered a broken vertebra in her back.
Last Monday, in a sprint car race at Ohsweken Speedway in Ontario, Stewart rolled his car five times but walked away. He stayed at the track to compete in the World of Outlaws race the next night and bristled at the NASCAR event at Pocono Raceway last weekend when asked about his harrowing incident in Canada.
"You mortals have got to learn, you guys need to watch more sprint car videos and stuff," he said Friday at Pocono. "It was not a big deal. It's starting to get annoying this week about that. That was just an average sprint car wreck. When they wreck, they get upside down like that."
Stewart gave an impassioned defense of sprint car racing in June following the death of good friend Jason Leffler, who was killed in an accident at Bridgeport Speedway in Swedesboro, N.J.
"I'd be grateful if you guys would understand that what happened this week wasn't because somebody didn't do something right with the racetrack. It was an accident. Just like if you go out and there's a car crash. It's an accident," Stewart said days after Leffler's death. "Nobody as a track owner wants to go through what happened, but it's not due to a lack of effort on their part to try to make their facilities as safe as possible under the conditions they have."
On Sunday, veteran sprint car driver Kramer Williamson died from injuries suffered during a qualifying race at Lincoln Speedway in central Pennsylvania. Williamson, 63, of Palmyra, was pronounced dead at York Hospital from serious injuries suffered in a crash that occurred Saturday night during the United Racing Company 358/360 Sprint Car Challenge.