Rosberg claimed his eighth pole of the season with a time of 1 minute, 32.506 seconds at Suzuka, 0.197 seconds ahead of Hamilton. Williams' driver Valtteri Bottas was third followed by teammate Felipe Massa.
"It was great today, but that's only one step on the way," Rosberg said. "It was a real pleasure because the car is so amazing to drive."
Hamilton leads Rosberg by three points in the overall title race — 241 vs. 238. Neither driver has ever won at Suzuka.
"''I wasn't really feeling it today, don't know why," Hamilton said.
Ferrari driver Fernando Alonso was fifth and Red Bull driver Daniel Ricciardo, who is a distant third in the championships race, qualified sixth for the race which is expected to be affected by a powerful typhoon in the region.
While wet races can throw up unexpected results, Rosberg believed rain may compound Mercedes' dominance.
"We are expecting it to be wet," Rosberg said. "Our last experience in the wet was at Spa where the car was very quick. So I'm very optimistic, even if it rains. It could be even better."
Despite crashing at the end of the morning practice session, Hamilton set the early pace in Q1 after his team worked frantically to repair the damage to his car in time for qualifying.
But Rosberg was fastest in the second qualifying session. Bottas briefly seized the lead in Q3 but Rosberg quickly grabbed it back on his final run.
Saturday's qualifying was overshadowed by news earlier in the day that four-time defending champion Sebastian Vettel would be leaving Red Bull at the end of the 2014 season for a possible move to Ferrari.
Vettel, who has won four of the past five races at Suzuka, has yet to win this season and finished ninth behind McLaren drivers Kevin Magnussen and Jenson Button.