Gordon took over the lead with eight laps left and held off Kyle Busch, beating him by more than 1 second to claim his first win since April 2009.
It was the 83rd career victory for Gordon, boosting him into a tie with Cale Yarborough for fifth place on the Sprint Cup series' all-time winners list.
Busch, meanwhile, came up a bit short in his bid to win all three NASCAR races at Phoenix. He was coming off victories in Friday's Camping World truck event and Saturday's Nationwide race.
Jimmie Johnson finished third, Kevin Harvick came in fourth and Ryan Newman rounded out the Top 5.
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