NASCAR inspectors said his Chevrolet was almost an inch too low but blamed it on a part failure _ not cheating. He was not stripped of the victory.
"We feel it was unintentional, and actually fairly unsafe," said NASCAR competition director Robin Pemberton. "We feel that it was a part failure, and we feel that it was unitentionally done. I think it would be marginal at best if there was any advantage.
"I am 100 percent sure this is unintentional."
NASCAR said it believed a mechanic made a mistake when the shocks were installed before the race.
Gordon's was the sixth team in three days to be caught with technical violations. The earlier problems led to expulsions, suspensions, fines and loss of championship points _ and the season hasn't even begun.
The most serious of the violations was committed by the new team of Michael Waltrip, whose Toyota failed inspection after an illegal substance was found in the gas line. His crew chief and team director were suspended indefinitely and kicked out of Daytona International Speedway. Waltrip was docked 100 driver and car owner points.
That was on the heels of lesser violations by the teams of Matt Kenseth, Kasey Kahne, Elliott Sadler and Scott Riggs, whose crew chiefs all were fined and suspended. All drivers also lost points.
"You couldn't stage this stuff, even if you wanted to," Pemberton said.
Roush Fenway Racing president Geoff Smith said the team "clearly" is going to file an appeal for the penalty assessed to driver Matt Kenseth earlier in the week, on the basis that NASCAR's system of assessing penalties is inconsistent.
"I'm sitting here, and Michael Waltrip gets two thirds the penalty of the last fuel additive alteration situation, and (Kenseth) got an unprecedented, never-seen-before penalty," Smith said. "Now you've got Jeff Gordon, who gets absolutely nothing for a deal that was similar to ours."
Gordon learned his car had failed inspection while finishing his post-race news conference.
"Are you serious? That sucks. I'm mad about that right now," he said with a look of disbelief on his face.
Asked what the penalty should be, Gordon wasn't sure.
"I mean, what do I think it should be? It's whatever NASCAR decides for it to be. That's what it should be. I mean, I think I should start the Daytona 500 on Sunday, but where I start will be the other thing.
Turns out that will be next to last.
"We're not going to take a win away from anybody," Pemberton said.
Tony Stewart was the day's first winner, taking the first 150-mile qualifying race to firmly establish himself as the Daytona 500 favorite. There were no questions about his victory as he easily held off former 500 winner Dale Earnhardt Jr. in the closing laps.
To add the Daytona 500 to his 11 other Daytona wins, Stewart likely will have to beat Earnhardt. It's expected that three-time Daytona winner Gordon, who charged from fourth to first on the final lap of the second race, still will be a top challenger, even starting from the rear.
Stewart said he gladly would give up his other Daytona wins for a triumph Sunday.
"Yeah, the qualifying races and the Shootouts and the July race are great, but I really want this race on Sunday badly," he said.
Four drivers _ two from each race _ raced their way into the lineup Thursday, including Michael Waltrip, who got what he wanted _ a chance to prove he didn't need to cheat to make the 500.
With an eighth-place finish, Waltrip and Boris Said, who nosed out Mike Bliss for 12th, advanced in the first qualifying race. They'll be joined in the 500 by Joe Nemechek and Mike Wallace, who finishe ninth and 11th in the second race.
Kyle Busch led most of the second race but lost the lead to his older brother Kurt, the 2003 series champion, and fell all the way to sixth on the 54th lap. Meanwhile, Gordon hung around the leaders throughout the race but seemed to come out of nowhere for the victory.
He pitted for two tires during a caution period 10 laps from the end, while the eight cars in front of him stayed on track. Gordon was 11th on the restart on lap 54 and slowly moved back into contention.
Gordon said it took some luck and some drafting help from J.J. Yeley to get to the front on the final trip around the 2.5-mile oval.
Kurt Busch wound up second, followed by David Stremme, Kyle Busch and former series champion Matt Kenseth, who raced from the rear of the 30-car field after his qualifying speed Sunday was disqualified.
The first race was slowed by six caution flags, while there were only two in the second 150.
For a while, it looked as if James Hylton, the 72-year-old hoping for a comeback at Daytona, would make the field for his first Daytona 500 since 1983. After running as high as second by staying on the track when others pitted during a caution, he got shuffled back on a late restart and faded out of contention.
Others who failed to make the race included former open-wheel star A.J. Allmendinger, his teammate Brian Vickers, two-time Daytona winner Bill Elliott, 2002 Daytona 500 winner Ward Burton and 1990 winner Derrike Cope.
AP Auto Racing Writer Jenna Fryer, and AP Sports Writers Mark Long and Chris Jenkins contributed to this report.