The former Sprint Cup champion backed up Saturday's Nationwide Series win at New Hampshire Motor Speedway with a Sprint Cup win there Sunday.
Through a postponement Saturday night and more delays Sunday, the car made famous by Richard Petty, won a race in NASCAR's top series for the first time since 1999.
Carl Edwards took the lead on a restart with 25 laps remaining and seemed to have the win wrapped up, but five-time Sonoma winner Jeff Gordon nearly chased him down on the final lap.
Through rain and a green-white-checker finish, Brendan Gaughan held on to win his first NASCAR Nationwide race in 98 starts.
The six-time series champion won Sunday for the first time in 25 Cup starts at Michigan International Speedway.
Ryan Hunter-Reay has become the first American to win the Indianapolis 500 since 2006, making a dramatic pass of Helio Castroneves on the final lap to win Sunday's race in the second-closest finish in history.
Helio Castroneves is poised to win a record-tying fourth Indianapolis 500 this year, but he will have plenty of competition from throughout the 33 car field.
Denny Hamlin, winner of three races at Daytona that didn't count, finally has a points-paying victory at a restrictor-plate track.
Ryan Hunter-Reay deftly guided his car around the rain-soaked track, stayed out of trouble and wound up with a much happier ending.
With a last-lap pass of Jeff Gordon in NASCAR's version of overtime, Joey Logano became the seventh different winner in as many races this season, with new rules for the championship Chase putting an increased emphasis on winning.