MotoGP rookie Jorge Lorenzo took his fourth pole position of the 2008 season, but first since April's Portuguese Grand prix, at Motegi on Saturday.
Lorenzo went on to claim his first and so far only MotoGP victory from pole at Estoril, while his Japanese qualifying triumph marked Michelin's first pole position since May's French GP with Dani Pedrosa - ten rounds previously.
A frantic conclusion to the qualifying hour saw Lorenzo prevail by 0.288secs from Ducati's world champion Casey Stoner, with outgoing Repsol Honda rider Nicky Hayden leading the RCV challenge in third.
Lorenzo's Bridgestone-shod Fiat Yamaha team-mate Valentino Rossi, who can clinch the 2008 MotoGP World Championship with third place even if Stoner wins on Sunday, will start from fourth on the grid, with Pedrosa fifth on his Bridgestone-backed pneumatic RC212V.
Loris Capirossi upheld Suzuki pride with sixth, albeit 0.9secs from pole, whilst Colin Edwards - who had snatched pole with 23 minutes remaining - collected seventh for Tech 3 Yamaha.
Randy de Puniet was the top satellite Honda rider in eighth for LCR, with Gresini's Shinya Nakano ninth in front of his home fans and Motegi rookie James Toseland tenth.
John Hopkins was the top Kawasaki challenger in eleventh, one place in front of former Suzuki team-mate Chris Vermeulen, with 2009 Repsol Honda rider Andrea Dovizioso a disappointing 14th for JiR.
Alice team-mates Toni Elias and Sylvain Guintoli will start 14th and 15th, with Stoner's team-mate Marco Melandri 16th - almost two seconds from pole - and Kawasaki's Anthony West 17th.
Gresini rookie Alex de Angelis fell on the exit of the final turn during the final minute and will start 18th, ahead of only Suzuki wild-card Kousuke Akiyoshi.
8. de Puniet
18. de Angelis