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While Schumacher moved a step closer to an unprecedented eighth world championship before retirement, his Renault title rival Fernando Alonso qualified only fifth.
World champion Alonso, who is level on points with Schumacher but behind 7-6 on race wins, will have his work cut out with the Toyotas of Ralf Schumacher and Italian Jarno Trulli between him and the Ferraris.
With two races remaining, including Sunday's showdown, Schumacher will take the title at Suzuka if he wins and Alonso finishes behind the 8th position.
Italian Giancarlo Fisichella, in the second Renault, starts alongside Alonso.
McLaren, which may end the season without a win for the first time since 1996, failed to get either of their cars into the top 10.
Kimi Raikkonen, Schumacher's replacement at Ferrari next season and last year's winner at Suzuka from 17th place on the starting grid, qualified 11th.
Spanish team mate Pedro de la Rosa was 13th.
Polish rookie Robert Kubica ended his 100 percent record of qualifying in the top 10 with 12th place for BMW Sauber in his fifth grand prix start.
Japan's Sakon Yamamoto, who finished a grand prix for the first time in China last weekend, failed to set a timed lap at his home circuit and starts last for Super Aguri.