Stewart has won 19 times at Daytona International Speedway but is now winless in his 15 career starts at the Daytona 500.
"Happy with our car, was just waiting for it to all get sorted out again," Stewart said. "I don't know what started it, but we just got caught up in another wreck."
Stewart won Saturday's Nationwide Series race that was marred by a last-lap crash that left 28 fans injured, giving him seven Daytona wins in NASCAR's second-tier series.
But in the big one, Stewart's futility is starting to rival that of the late Dale Earnhardt, who didn't win the Daytona 500 until his 20th try in 1998.
"If I told you I wasn't heartbroken, I'd be lying to you," Stewart said earlier in a TV interview.
Harvick was hoping to become the first driver to win the Sprint Unlimited, a qualifying race and the 500.
"I let off a little bit to miss the wreck," Harvick said. "It looked like the No. 18 (Kyle Busch) hooked the No. 5 (Kasey Kahne), and that kind of just started a chain reaction. I don't know who was behind me, but just one of those deals."
The wreck started when Kahne lost control and spun across the track on lap 34. Harvick crashed when reigning Sprint Cup champion Brad Keselowski tried to avoid the wreck.
Kyle Busch remained on the lead lap.