Formula One's two Japanese carmakers shared the front row for the first time, with Briton Jenson Button second for Honda-powered BAR.
McLaren, who lead Renault by two points in the constructors' standings with one race remaining after Japan, will have to fight from the rear after rain played havoc with their qualifying hopes.
Kimi Raikkonen, who has a 10-place penalty for an unscheduled engine change in Friday's practice, was 17th.
Colombian Juan Pablo Montoya was classified 18th but he, Toyota's Jarno Trulli and Jordan's Tiago Monteiro failed to set a time.
"We've never worked so hard to come so low on the grid," declared team boss Ron Dennis, who said Raikkonen will still start 17th rather than last because "you can only lose 10 places against someone who set a time."
McLaren's hopes of clinching the title in Suzuka depend on them finishing first and second with Renault scoring no more than 1 point. Otherwise the battle will be decided in Shanghai next weekend.
Renault's newly-crowned champion Fernando Alonso qualified 16th but Italian Giancarlo Fisichella raised the French manufacturer's hopes of clawing back the lead with a second row position.
MCLAREN STRENGTH
Button said he expected McLaren, winners of the last five races, to come through regardless.
"We will do everything we possibly can to have the best race we can but we've seen before, when Kimi has started at the back or Juan Pablo, that they are very strong -- especially on a circuit like this.
"I think we will see them coming through the field very quickly," said the Briton, who will be making his 99th start still in search of a first win.
"But we can't go into this race feeling defeated already. We have to stay positive and look for the win, definitely."
Ralf recognised that he had been lucky, benefiting from a drier track than the later runners. "Giancarlo would have gone a lot faster anyway, we could see that," he said.
"It feels great," said the German. "Being in Japan, on a circuit I like, with Toyota for the first time here, first time on pole, so it's a great result for the team."
The pole was the sixth of Ralf's career but first for Toyota, the team he joined from Williams at the end of last year. It could also be considered Toyota's first 'proper' one.
EMPTY TANK
Italian Jarno Trulli was fastest at Indianapolis in June but on an almost empty tank as it became apparent that the Michelin-equipped teams would not race due to tyre safety concerns. He did not start on the Sunday.
Fisichella was also fortunate, just as he was in the Australian season-opener that he won, by going out for his qualifying lap just as the weather turned.
"I feel confident, I feel right," he said. "Obviously it would be nice to win the race, I think we have a good chance."
The Italian will share the second row with Austrian Christian Klien in a Red Bull, who qualified fourth.
Japan's Takuma Sato, in a BAR, was fifth with Briton David Coulthard alongside for Red Bull.
Ferrari's seven-times champion Michael Schumacher, winner four times in the last five years at Suzuka, starts 14th with Brazilian team mate Rubens Barrichello ninth.
"Basically all I could do was swim for home," said Schumacher, who crashed in practice. "I think it is fair to claim I was hit with bad luck today.
The slippery conditions also proved tricky for several early runners, with Trulli and Monteiro both spinning into the gravel at turn nine. Brazilian Antonio Pizzonia spun at the same point but kept his Williams on track and qualified 12th.
