German Rosberg, who trails Hamilton by three points in the championship with five races remaining, lapped 0.197 seconds quicker than the Briton as the feuding rivals prepare to lock horns again in a race which could be threatened by typhoon rains.
It was his first pole in Japan and eighth of the Formula One season and an important boost after being forced to drop out of the Singapore Grand Prix two weeks ago and letting Hamilton in front.
"I’m not thinking about Singapore any more, only racing here and enjoying doing the job here," Rosberg told reporters.
"We're here at Suzuka and I'm trying to win. It was great today [Saturday] but that's only one step on the way.”
Hamilton, seeking a third successive pole, crashed in the morning practice, robbing him of the chance to test the faster, soft compound tyres.
"Rosberg was extremely quick and I did the best I could," said Hamilton. "But tomorrow [Sunday] is the day we get the points, so I’m looking ahead to the tricky weather forecast."
The two Mercedes men locked out the front row again, breaking Red Bull's five-year domination of pole at Suzuka on the day four-time defending champion Sebastian Vettel announced he will leave the team at the end of the year.
Vettel, who has won the Japan race four of the past five years, could only muster a distant ninth on the grid.
Finland's Valtteri Bottas was six-tenths down and third fastest for Williams behind the dominant Mercedes, ahead of teammate Brazilian Felipe Massa.
Two-times champion Fernando Alonso drove his Ferrari to fifth, while Australian Daniel Ricciardo will start alongside him in his Red Bull.
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