Johnson traveled around the 1 1/2-mile Texas Motor Speedway in 28.261 seconds. He nipped Greg Biffle by .103 of a second to capture the pole.
It was the second pole in as many weeks for Johnson, who after finishing first in qualifying at Martinsville, Va., went on to win the race and move past Brad Keselowski into first place in the championship race.
Johnson, trying to win the Sprint Cup title for the sixth time in seven years, has a two-point lead over Keselowski in what has become a two-driver race with three events remaining.
Keselowski will start eighth on Sunday.
Dale Earnhardt Jr., driving for the second week after missing two races with a concussion, qualified 18th.