Allmendinger traveled at a speed of 134.675 for one lap around the Phoenix International Raceway. His first pole came in his 87th Sprint Cup start.
"To get a pole, it might be minor," Allmendinger said. "But it's a victory for us. We've always struggled in qualifying."
Allmendinger's best Sprint Cup finish has been a third at last year's Daytona 500.
Scott Speed had the second-fastest qualifying effort, followed by Sam Hornish, Marcos Ambrose and Dale Earnhardt, Jr. It was the best qualifying showing in Hornish's career.
Four-time defending series champion Jimmie Johnson qualified 16th. Mark Martin, who won here last year, was 23rd.