Marlin had his Dodge Intrepid tapped from behind by Jerry Nadeau on lap 120 of the 267-lap event while heading toward a pit stop.
As Marlin was spun around, he could not control his car's speed on pit lane and passed the limit. But NASCAR could not communicate in time to hold him for the penalty, which was waved off after his exit.
Marlin, who started the year with an eighth-place finish at Daytona and was second last week at Rockingham, took his ninth career Winston Cup checkered flag. He led the final 30 laps after passing Jeremy Mayfield's Dodge on a late restart.
"When I saw that caution, I said, `Oh no, not again,'" said Marlin, who during the Daytona 500 got out of his car during a red-flag stop to pull the fender on his right front tire -- a violation of the rules which cost him a chance to win the race. "Everybody didn't pit then because track position means so much. It worked out great."
Marlin averaged 136.754 miles per hour and crossed the finish line 1.163 seconds ahead of Mayfield. His victory came in front of a crowd of 137,500, the largest for a sporting event in Nevada.
Tony Stewart was in the lead prior to that pit cycle and had a chance to win a $1 million bonus for himself and a lucky fan as part of NASCAR's "No Bull" promotion. But he finished fifth in a Pontiac Grand Prix behind the Ford Tauruses of Mark Martin and rookie Ryan Newman.
"We were strongest at the end and that was good," Martin said. "The car was not good enough to win with today, but we made the best of it at the end."
Stewart came out of his stop sixth when Mayfield took only two tires and fuel. Marlin grabbed four fresh tires and, with a better car, did not take long to pass Mayfield, who settled for runner-up.
"We probably got faster than anyone out there," Mayfield said. "We were real good on long runs, but we never got up on track position because we kept losing so much at the beginning."
Stewart and Marlin each led a race-high four times.
"We probably had a 10th-place car," Marlin said. We decided to go for the win. We changed it up and hit right on it with the shocks and springs."
A two-time Winston Cup winner in Las Vegas, Burton also won Saturday's Busch series race from the pole.