Jorge Lorenzo produced a track record late in the session to snatch pole away from MotoGP title rival Dani Pedrosa for Sunday's race in Japan.
Repsol Honda rider Pedrosa's time of one minute 45.215 seconds looked set to earn him pole position, boosting his chances of closing the 33-point gap behind his fellow Spaniard at the top of the standings.
But Lorenzo scorched round the Motegi circuit in 1min 44.969sec shortly before the end of the session to place his factory Yamaha at the front of the grid.
Great Britain's Cal Crutchlow did very well to stay on his Monster Tech 3 Yamaha, rescuing what looked set to be a crash and finishing third fastest to complete the front-row line-up.
Yamaha's Ben Spies follows in fourth despite a late crash and is joined on row two by Alvaro Bautista (San Carlo Honda Gresini) and Crutchlow's team-mate Andrea Dovizioso.
Casey Stoner's first race back after injury will start from seventh place, with Stefan Bradl - who recovered from a bad crash to return to the track - and Valentino Rossi joining him on the third row.
Rossi's Ducati team-mate Nicky Hayden, struggling with a fracture in his right arm, was 10th.
