Mark Martin qualified fourth, and Dale Earnhardt Jr. was seventh. Defending Cup champion Brad Keselowski was ninth.
Johnson has never won in 23 Cup races at Michigan.
“Of course we wanted to be a little bit better, but we had a very smooth and clean practice session made some good changes to the car and found speed as the session went on,” Johnson said. “Came close to getting another pole during qualifying, so all in all just really good.”