Jarrett recorded his 29th career victory and first since New Hampshire last July, a span of 30 races.
Rudd appeared headed for victory after taking the lead from Jeff Burton on the 179th lap at Pocono Raceway, but Rudd's right-rear tire started to go flat.
A few laps later, he went into a wall, bringing a caution, under which the race ended. It marked the second straight week Rudd had dropped out of contention after experiencing tire trouble.
"I'm glad we're here," Jarrett said, "but I hate it for Ricky. Our cars were about even. He is going through a tough stretch right now."
Mark Martin finished second with rookie Jimmie Johnson taking third. Completing the top 10 were points leader Sterling Marlin, Jeff Gordon, Burton, Tony Stewart, Michael Waltrip, Rusty Wallace and Dave Blaney.
Martin found himself in position to win the race when, running in the top five, he was the only one among the leaders who could make it to the end without stopping for fuel.
But a caution flag came out for debris on the track with about 35 laps remainnig, allowing the front runners to make a quick stop for tires and fuel.
"We were in great shape until that mystery caution came out," Martin said. "We could have won the race the way things were going."