As Stewart dodged the crash and crossed the finish line, the front clip of Larson's car sheared off , ripping the engine out of its compartment. The front suspension and engine ended up on the walkway at the bottom of the stands.
A tire from Larson's car also flew into the grandstands.
Regan Smith led as the cars approached the checkered flag, but Smith tried to block Brad Keselowski, who was running second, and turned across the nose of Keselowski's car.
There were no immediate reports as to the extent of injuries, but emergency medical personnel arrived on the scene with stretchers and removed one spectator who was tightly strapped to the gurney. Other fans appeared to be receiving treatment at the scene.
The emergency in the grandstand tempered Stewart's fifth victory in his last six February races at Daytona and the 11th Nationwide Series win of his career.
"Fortunately, with the way the event's equipped up, there were plenty of emergency workers ready to go, and they jumped in on it pretty quickly," NASCAR president Mike Helton told ESPN. "And right now, it's just a function of trying to determine what all damage is done.
"They're moving folks, as we've seen, to care centers and taking some folks over to Halifax Medical (Center), so we'll be able to update later on, but right now, all we know is everybody's working real hard on determining what all happened."
Larson climbed from his car almost immediately and was evaluated and released from the infield care center.
Drivers, Larson included, were more concerned with the safety of the fans than the outcome of the race.
"The important thing is what's going on on the frontstretch right now," Stewart said after climbing from his car. "We've always known since racing was started this is a dangerous sport. But it's hard. We assume that risk. It's hard when the fans get caught up in it.
"As much as we want to celebrate right now, as much as this is a big deal to us, I'm more worried about the drivers and fans in the stands right now. I could see it all in the mirror and it didn't look good from where I was either."
Smith said he wasn't about to surrender the victory to Keselowski 200 yards from the finish line.
"We made a move to try and win the race," Keselowski said. "We were in the catbird seat. Regan was in a good spot. He was first and I was second, and we were pushing. I kind of had the run and the move to win the race, and Regan obviously tried to block it, and that's understandable.
Sam Hornish Jr. crossed the stripe in second place, followed by rookie Alex Bowman, Dale Earnhardt Jr. and Parker Kligerman.
The last-lap wreck wasn't the only serious incident of the event. A 13-car wreck in Turns 1 and 2, triggered by contact between the No. 43 Ford Mustang of Michael Annett and the No. 3 Chevrolet Camaro of Austin Dillon -- both championship hopefuls -- stopped the race after 116 laps and set up the finish.
Annett was transported to Halifax Health Medical Center. Richard Petty Motorsports later reported that Annett, whose car slammed the outside wall nose-first, was treated for bruising on his chest and received a CT scan. He remains in the hospital for further observation.
1. (10) Tony Stewart(i), Chevrolet, 120, $109220.
2. (2) Sam Hornish Jr., Ford, 120, $99378.
3. (8) Alex Bowman #, Toyota, 120, $85603.
4. (13) Dale Earnhardt Jr.(i), Chevrolet, 120, $68635.
5. (3) Parker Kligerman, Toyota, 120, $69838.
6. (29) Brian Scott, Chevrolet, 120, $64013.
7. (14) Justin Allgaier, Chevrolet, 120, $61713.
8. (28) Eric McClure, Toyota, 120, $60638.
9. (30) Robert Richardson Jr., Chevrolet, 120, $59388.
10. (4) Travis Pastrana, Ford, 120, $59713.
11. (17) Nelson Piquet Jr. #, Chevrolet, 120, $57338.
12. (11) Brad Keselowski(i), Ford, 120, $50495.
13. (21) Kyle Larson #, Chevrolet, 120, $56488.
14. (15) Regan Smith, Chevrolet, 120, $51995.
15. (6) Elliott Sadler, Toyota, 120, $57538.
16. (9) Matt Kenseth(i), Toyota, 120, $51095.
17. (27) Mike Harmon, Dodge, 120, $55413.
18. (33) Joe Nemechek, Toyota, 120, $55188.
19. (20) Brian Vickers, Toyota, 118, $48595.
20. (19) Kasey Kahne(i), Chevrolet, 118, $49145.
21. (5) Austin Dillon, Chevrolet, 117, $54813.
22. (31) Jeffrey Earnhardt #, Ford, Accident, 116, $55088.
23. (26) Mike Bliss, Toyota, Accident, 116, $54513.
24. (35) Jason White, Toyota, Accident, 116, $54388.
25. (38) Danny Efland, Chevrolet, Accident, 116, $54713.
26. (22) Michael Annett, Ford, Accident, 115, $54113.
27. (25) Johanna Long, Chevrolet, Accident, 115, $54013.
28. (32) Hal Martin #, Toyota, Accident, 115, $53913.
29. (18) Jamie Dick, Chevrolet, Accident, 115, $47345.
30. (39) Reed Sorenson, Chevrolet, Engine, 102, $53988.
31. (1) Trevor Bayne, Ford, 101, $57413.
32. (7) Kyle Busch(i), Toyota, Engine, 100, $46970.
33. (37) Jeremy Clements, Chevrolet, Oil Line, 88, $53388.
34. (23) Mike Wallace, Chevrolet, 87, $53338.
35. (40) Kurt Busch(i), Chevrolet, Accident, 65, $46702.
36. (12) Danica Patrick(i), Chevrolet, Engine, 31, $42185.
37. (36) Juan Carlos Blum #, Ford, Accident, 30, $42120.
38. (34) Blake Koch, Toyota, Overheating, 14, $42059.
39. (24) Scott Lagasse Jr., Chevrolet, Accident, 7, $40960.
40. (16) Jeff Green, Toyota, Vibration, 4, $40910.