Rosberg set a time of 1:32.584 to finish 0.076s clear of Lewis Hamilton, who made a mistake at the hairpin, and the drivers were denied a final flying lap following a huge crash for Red Bull’s Daniil Kvyat.
Kvyat lost control of his Red Bull RB11 after dipping a wheel onto the grass on the approach to the hairpin and slammed into the barriers, flipping his car in the process, though he was able to walk away uninjured.
The session was halted and with only half a minute remaining it was not restarted, enabling Rosberg to take top spot.
Valtteri Bottas was third for Williams as he edged ahead of Ferrari’s Sebastian Vettel.
Felipe Massa and Kimi Räikkönen will line-up on the third row of the grid, in front of Daniel Ricciardo.
Romain Grosjean was eighth for Lotus while Sergio Pérez did not set a time in ninth position, ahead of Kvyat.
Nico Hülkenberg was 11th for Force India but drops three places as a result of his penalty for colliding with Massa in Singapore.
Carlos Sainz Jr. therefore moves up to 11th place on the grid, in front of Pastor Maldonado and Fernando Alonso.
Max Verstappen was 15th after stopping on circuit during the closing stages of Q1 due to a loss of power and therefore was unable to participate further in qualifying.
Jenson Button qualified outside of the top 10 at Suzuka for the first time in his career as he collected 16th place, having been in the wrong engine setting on his opening run, ahead of several drivers who felt Verstappen’s stoppage cost them their best lap.
Marcus Ericsson was 17th position having spun at Spoon early in the session, while Sauber team-mate Felipe Nasr was also eliminated.
Manor Marussia pair Will Stevens and Alexander Rossi completed the Q1 runners.