The German, who will be bidding for his sixth Suzuka victory on Sunday, clocked one minute 47.906 seconds in heavy rain, more than 16 seconds slower than Ferrari team mate Rubens Barrichello's pole-setting time last year.
Sauber driver Giancarlo Fisichella of Italy was second fastest with a time of 1:48.362, with Brazilian Barrichello third in 1:49.846 as only 17 drivers set lap times in the treacherous conditions.
Briton Jenson Button was fourth quickest but BAR team mate Takuma Sato disappointed the home fans by stopping after one lap and failing to set a time.
Japanese Sato briefly lost control on returning to the pit lane and opted for caution by not coming back out.
Jaguar driver Mark Webber of Australia also skidded approaching the pits and was one of eight drivers who did not set times, including Brazil's Felipe Massa (Sauber), who spun off into a crash barrier at turn eight.
Sunday's race could be disrupted by typhoon "Ma-on", forecast to hit central Japan this weekend.
