Andrea Dovizioso upheld Honda honour superbly in the absence of his injured team-mate Dani Pedrosa by taking the first pole of his MotoGP career at Motegi.
The Italian only had one front row start to his name at the top level prior to today's session, but established himself on provisional pole mid-way through.
Although Ducati's Casey Stoner briefly deposed Dovizioso with five minutes to go, the Honda rider - who will lose his factory seat to Stoner next year unless the team adds a third works bike - immediately struck back and reclaimed the top spot less than a minute later.
Valentino Rossi came closest to toppling Dovizioso, falling 0.054 seconds short as the world champion took second place, his best starting position since returning to MotoGP following his mid-season leg injury.
Rossi's late improvement pushed his Yamaha team-mate and championship leader Jorge Lorenzo back to fourth - the first time all year the Spaniard has missed the front row, though he was still within 0.2s of pole as he used the latest Yamaha engine for the first time.
The Tech 3 Yamahas completed the top six, Colin Edwards emerging ahead of Ben Spies after a close late battle that saw them on equal times for a while.
Their improvements knocked LCR Honda's Randy de Puniet back from fifth to seventh in the closing moments, while Marco Simoncelli (Gresini Honda) made a late jump into eighth.
Suzuki got both bikes into the top 10 for its home race, though ninth and 10th for Alvaro Bautista and Loris Capirossi was a slight anti-climax after this morning's top six results. Capirossi had an early fall but soon rejoined on his spare bike.
Nicky Hayden struggled on the second works Ducati and was only 11th, while home rider Hiroshi Aoyama (Interwetten Honda) could not repeat his Friday form and will start 14th.
Pos Rider Team Time Gap 1. Andrea Dovizioso Honda 1m47.001s 2. Valentino Rossi Yamaha 1m47.055s + 0.054s 3. Casey Stoner Ducati 1m47.105s + 0.104s 4. Jorge Lorenzo Yamaha 1m47.206s + 0.205s 5. Colin Edwards Tech 3 Yamaha 1m47.464s + 0.463s 6. Ben Spies Tech 3 Yamaha 1m47.648s + 0.647s 7. Randy de Puniet LCR Honda 1m47.752s + 0.751s 8. Marco Simoncelli Gresini Honda 1m47.914s + 0.913s 9. Alvaro Bautista Suzuki 1m48.002s + 1.001s 10. Loris Capirossi Suzuki 1m48.068s + 1.067s 11. Nicky Hayden Ducati 1m48.182s + 1.181s 12. Marco Melandri Gresini Honda 1m48.238s + 1.237s 13. Aleix Espargaro Pramac Ducati 1m48.371s + 1.370s 14. Hiroshi Aoyama Interwetten Honda 1m48.396s + 1.395s 15. Hector Barbera Aspar Ducati 1m48.535s + 1.534s 16. Mika Kallio Pramac Ducati 1m49.480s + 2.479s