The Swiss led from the first lap of the second qualifying phase at the Japanese circuit, with his time of 53.443 seconds enough to see him on pole for the third time this season.
Team-mate and championship leader Yvan Muller was second, 0.049secs back, although Robert Dahlgren (Polestar Volvo) pipped Rob Huff to prevent a Chevrolet one-two-three.
Tom Coronel in his ROAL BMW was fifth, ahead of the Sunred Seats of Tiago Monteiro, Michel Nykjaer and Gabriele Tarquini.
Darryl O'Young (Bamboo Chevrolet) will be on pole for race two, ahead of Coronel, Huff and Muller.
Muller leads the drivers' championship by 16 points from Huff, with Menu third.