Valentino Rossi will start the Japanese MotoGP from pole position to head up a heavyweight front row with Marc Marquez and Jorge Lorenzo at Motegi.
Championship leader Marquez had occupied provisional pole with less than one minute remaining with a time of 1m 44.134s.
But Marquez scuppered a flying lap in the closing moments after getting out of shape on the brakes and his final effort was hampered when he was forced to slow as marshals retrieved British rider Cal Crutchlow's fallen bike on his last attempt.
"In the second run I was able to be faster, but I made a small mistake on the first lap and on the second I saw the yellow flag for Crutchlow," Marquez confirmed. Maybe I was able to push a little bit more but after seeing the crash of Dani and Jorge it was better to take care."
Nearest title rival Rossi powered through with a scorching time on the Movistar Yamaha, climbing from sixth place to clinch his 64th GP pole on his final lap by almost two tenths - the same number of GP poles as fierce rivals Marquez and Lorenzo.
The nine-time world champion, who trails Marquez by 52 points with four races including the Japanese round remaining, lapped in 1m 43.954s to secure pole by 0.180s.
Marquez – fastest in both FP3 and FP4 prior to qualifying – will take up his place on the front row flanked by reigning world champion Lorenzo on the second of the factory Movistar Yamaha machines, who was cleared to continue racing after undergoing a CT scan following a huge high-side in FP3. Lorenzo was 0.267s behind team-mate Rossi to complete a formidable front row in Japan.
Andrea Dovizioso heads up row two on the factory Ducati GP16, lapping in 1m 44.294s as the Italian finished more than three tenths off Rossi's pace.
Dovizioso is joined on the second row by Crutchlow, who slotted into fifth despite his late fall on the LCR Honda, while Aleix Espargaro managed to turn the tables on Maverick Vinales to finish as the top Suzuki rider with a fine lap in 1m 44.494s to snatch sixth ahead of the Silverstone race winner by 0.045s.
Vinales leads the third row from Hector Barbera, who impressed in eighth place as the Spaniard replaces injury victim Andrea Iannone in the factory Ducati team on the GP16 at Motegi. Barbera's best lap in 1m 44.980s put him ahead of Pol Espargaro on the Monster Tech 3 Yamaha.
Pramac Ducati duo Danilo Petrucci and Scott Redding were 10th and 11th quickest as they prepare for the next stage of their points battle in Japan to seal a ride on the new GP17 next season, with Alvaro Bautista completing the top 12 on the Gresini Aprilia RS-GP. Bautista dramatically fell on his out lap in Q2 and never posted a time after topping Q1 from Redding.
The returning Bradley Smith, fit again after suffering a knee injury in August in a fall during practice for the Oschersleben 8-Hour race, was 15th behind Stefan Bradl (Gresini Aprilia) and Aussie Jack Miller, who is also back in action this weekend on the Marc VDS Honda after recovering from injury.
Yamaha test rider Katsuyuki Nakasuga was 16th fastest on the factory Yamalube Yamaha M1 and starts from row six with Yonny Hernandez (Aspar Ducati) and Tito Rabat (Marc VDS Honda).
Hernandez's team-mate, Eugene Laverty, qualified in 19th place after being passed fit to race in the wake of a massive high-side on Friday in FP2. The Irish rider leads the seventh row from Avintia Racing's Loris Baz and Mike Jones, who takes over Hector Barbera's seat in the team as the 2015 Australian Superbike champion makes his premier class bow.
Japan's Hiroshi Aoyama, who will stand in for Dani Pedrosa in the Repsol Honda team after the Spaniard was ruled out with a broken collarbone due to a massive high-side on Friday, brings up the rear of the grid.
1. Valentino Rossi
2. Marc Marquez
3. Jorge Lorenzo
4. Andrea Dovizioso
5. Cal Crutchlow
6. Aleix Espargaro
7. Maverick Viñales
8. Hector Barbera
9. Pol Espargaro
10. Danilo Petrucci
11. Scott Redding
12. Alvaro Bautista
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