Kasey Kahne captured the pole for the season-ending Ford 400 at Homestead-Miami Speedway, but the focus was on how the three drivers with a chance to win the championship would qualify.
Hamlin will take a 15-point lead over Johnson and a 46-point advantage over Kevin Harvick into the concluding race. It is the closest points race since NASCAR went to its current championship chase format in 2004.
Johnson qualified sixth while Hamlin will start 27th and Harvick 38th.
Kahne won the pole with a lap of 176.904 mph. It was his fourth pole of the season.
Hamlin said he was not discouraged by his poor qualifying run.
"Our car is going to be fine for (Sunday's race)," Hamlin said. "We know that. This is a track where you can pass, so we're looking forward to that part of it."
Hamlin won last year's race at Homestead after starting 38th.