It was the first time in 37 years the showcase of stock car racing had been shortened by rain and it added another bizarre chapter to an event that has grown into one of the most significant on the American sports calendar.
"You just don't know what Daytona means unless you have risked your life pursuing your dreams here," said an emotional Waltrip.
Waltrip captured the race in 2001, but that victory was overshadowed by the death of Dale Earnhardt, whose car hit the wall on the final turn of the final lap just as Waltrip was crossing the finish line.
It was Earnhardt who helped give Waltrip's fading career a boost by hiring him to race for his team.
"I'm so thankful for Dale Earnhardt," Waltrip said. "He made this place more special. I know he's smiling now. This place and he were one."
The win Sunday will likely be a controversial one since drivers and the more than 200,000 spectators had hoped to see a full 500-mile competition. Instead, the race was declared official after only 109 of the scheduled 200 laps around the Daytona International Speedway.
Although Waltrip would have been difficult to beat if the race had resumed, those close to the lead were deprived a chance to win their sport's biggest event.
Kurt Busch finished second with Johnson third and Kevin Harvick fourth. Veteran Mark Martin, who finished second in the season-long championship last year and who started near the back of the field Sunday, was in fifth place when the race was stopped.
Bad weather threatened the race from the start and it was stopped for more than an hour early in the day when a brief, but heavy shower moved through.
Race favorite Dale Earnhardt Jr. appeared set to dominate when the race resumed, but the battery failed in his Chevrolet and he lost two laps while his crew changed the battery.
Earnhardt, however, played a key role in the race as a second rainstorm began to close in on the track.
Johnson emerged from the pits with the lead after a caution flag, but even though Earnhardt was two laps down, he was just in front of the leaders on the track. Waltrip was able to pull in behind Earnhardt, his teammate, and the draft created by their working in tandem allowed Waltrip to breeze past Johnson.
The rains came soon after and NASCAR officials waited more than an hour before deciding the race would be called.
"If the rain had been there 10 minutes earlier, we would have won the Daytona 500," Johnson said. It's disappointing. But when Michael got under me and got by, it was all over."
This was the shortest Daytona 500, replacing the 1965 race won by Fred Lorenzen after 133 laps. In its 45-year history, the only other Daytona 500 not run to completion came in 1966, when Richard Petty was declared the winner with two laps to go.
"It's a bittersweet finish for us," said Busch, who started 36th and made it to second in a Ford Taurus. "We do most of this stuff under the radar on these restrictor-plate tracks. DEI (Dale Earnhardt Inc.) has something on these restrictor-plate tracks that nobody else really has."
DEI cars have won four of the last five races at Daytona. Waltrip scored his first Winston Cup win in the 2001 Daytona 500 and claimed last year's Pepsi 400. Earnhardt Jr. won the 2001 Pepsi 400 five months after his father's death.
The end of a long and frustrating day left all but the winner feeling a little empty.
"It's difficult to accept and to swallow," Busch said. "It's the biggest race of the year, but it was really up to the weather. It's kind of upsetting to see this race finish so soon."
Johnson led on lap 100 - the halfway point - when the race was restarted. But on lap 103, Mike Skinner's Chevrolet suffered a flat to bring out another caution. The race restarted on lap 106 with Johnson in the lead.
Christian Fittipaldi got a slow restart and that allowed Waltrip to get under Johnson and get a draft from the lapped car of Earnhardt to take the lead.
Defending champion Ward Burton spun out of the fourth turn of lap 107 for another caution. It then began to rain and two laps later the red flag stopped the race. After 69 minutes, NASCAR officials called it a complete race.
"Fair or not fair, I knew what the situation was going to be," Johnson said. "Dale Earnhardt Jr. is Michael's teammate and that is racing and what you have to do on restrictor-plate racing."
It was a race that never really developed any rhythm because of the weather concerns. The race was started 20 minutes early because heavy rain already had reached Florida's Gulf Coast, about 120 miles away.
Jeff Green started on the pole, but Waltrip quickly blew by him in the third turn of the first lap. Waltrip led the first 64 laps, which included a savage crash on lap 57 that involved Ryan Newman and Ken Schrader.
Newman's car hit the wall coming out of Turn 4 so hard, the rear axle ripped off his Dodge Intrepid. Newman's car then went airborne, made a backwards half flip onto the roof and pirouetted. The car dug into the grass and made 2 1/2 more flips before landing upside-down on the roof.
Newman was able to climb unhurt from under the wreckage. Schrader's car went across the grass and crashed into Bobby Labonte's car on pit road.
Rain started to fall on lap 61 and the red flag came out two laps later for 68 minutes.