YAMAHA rider Valentino Rossi took pole at the Japanese MotoGP on Saturday, with team mate Jorge Lorenzo recovering from a horrifying crash in practice to qualify third.

Rossi, second in the championship race 52 points behind Marc Marquez, lapped the Motegi circuit in one minute 43.954 seconds, ambushing the Spaniard late in a lively qualifying session.

Rossi's team mate Lorenzo earlier escaped serious injury after his bike high-sided near turn two and hurled him into the air before he slammed back down on his back.

The Spaniard was air-lifted to hospital for tests but returned to the track, shrugging off the pain to grab a front row spot next to Marquez on a day of glorious sunshine.

"I thought I injured my left foot but finally it was just a muscle problem," he said in trackside interview.

"I had a lot of pain ... I forgot about the crash and the pain.

"Rossi made a great, great lap time. But better than expected (for me) after the flight this morning."

Rossi, the seven-times premier class champion and runner-up last year, was thrilled to grab pole, having felt under the weather during the race weekend.

"I'm not at 100 percent, I'm a little bit sick," he said.

"When I saw 43.9 (seconds) I was very happy.

"It will be very important to start from pole tomorrow and we will see."

Marquez has an outside chance of clinching the championship on Sunday, but must win the race and have Rossi finish 15th or lower and Lorenzo no better than fourth.

He was in the box seat to take pole after posting a quick early lap but made errors on his later efforts as Rossi roared to the top of the timesheet in the final minute.

Ducati's Andrea Dovizioso will start fourth on the grid in front of fifth-placed Cal Crutchlow and Aleix Espargaro.