Casey Stoner edged out Yamaha rival Jorge Lorenzo to take his fourth consecutive pole position, his 10th of the season, at Motegi.
Qualifying proved to be an engrossing battle between Stoner, his Honda works teammate Dani Pedrosa and Lorenzo, with the trio often separated by less than 0.1sec.
Pedrosa was the first rider to dip below 1m46s, but as has so often been the case this season Stoner was able to respond, moving more than two tenths clear at the front. With five minutes to go, however, his position suddenly came under serious threat, as Lorenzo produced a stunning lap on the Yamaha to take provisional pole, beating his own 2008 lap record in the process.
Once again it was up to Stoner to respond, and while his first lap fell short his second flyer was phenomenal, the Australian eventually posting a 1m45.267s to shatter the lap record and move more than a quarter of a second clear. Lorenzo therefore had to settle for second, while Andrea Dovizioso - polesitter last year - demoted Pedrosa in the final minutes to capture the final spot on the front row.
Pedrosa will share the second row with Yamaha's Ben Spies and Gresini's Marco Simoncelli.
Spies, battling severe illness and sickness, improved throughout to seal fifth, while Simoncelli was able to seal sixth on his final lap, having lost his first bike when he dropped the front at Turn 5 in the first 25 minutes.
Simoncelli's gain was Valentino Rossi's loss, the Italian dropping to seventh having just set his own late flyer. Rossi was often troubling the top six however, hinting at real progress for Ducati.
Alvaro Bautista on the lone Suzuki finished in eighth, with Hector Barbera on the Aspar Ducati beating the works Ducati of Nicky Hayden to ninth.
There was a fall, too, for Tech 3's Colin Edwards, although like Simoncelli he was able to return and use a second bike, eventually finishing 14th fastest.
Pos Rider Team/Bike Time Gap
1. Casey Stoner Honda 1m45.267s
2. Jorge Lorenzo Yamaha 1m45.523s + 0.256s
3. Andrea Dovizioso Honda 1m45.791s + 0.524s
4. Dani Pedrosa Honda 1m45.966s + 0.699s
5. Ben Spies Yamaha 1m46.042s + 0.775s
6. Marco Simoncelli Gresini Honda 1m46.211s + 0.944s
7. Valentino Rossi Ducati 1m46.467s + 1.200s
8. Alvaro Bautista Suzuki 1m46.586s + 1.319s
9. Hector Barbera Aspar Ducati 1m46.694s + 1.427s
10. Nicky Hayden Ducati 1m46.763s + 1.496s
11. Hiroshi Aoyama Gresini Honda 1m46.811s + 1.544s
12. Cal Crutchlow Tech 3 Yamaha 1m46.818s + 1.551s
13. Randy de Puniet Pramac Ducati 1m46.917s + 1.650s
14. Colin Edwards Tech 3 Yamaha 1m47.165s + 1.898s
15. Karel Abraham Cardion Ducati 1m47.922s + 2.655s
16. Toni Elias LCR Honda 1m48.169s + 2.902s
17. Kousuke Akiyoshi LCR Honda 1m48.367s + 3.100s
18. Damian Cudlin Pramac Ducati 1m48.962s + 3.695s
19. Shinichi Ito Honda 1m49.971s + 4.704s