Yamaha rider Johann Zarco secured pole position on Saturday for the MotoGP Grand Prix of Japan.
Zarco clocked a time of 1 minute, 53.469 seconds to edge Ducati rider Danilo Petrucci by 0.318 seconds.
Championship leader Marc Marquez was third-fastest, 0.434 seconds off the pace.
Aprilia rider Aleix Espagaro was fourth followed by Ducati's Jorge Lorenzo.
Repsol Honda rider Dani Pedrosa, who has five wins at Motegi, was sixth. Ducati rider Dovizioso, who had the fastest lap in Friday's practice, finished ninth.
Nine-time former world champ Valentino Rossi qualified 12th.
With four races left, Repsol Honda rider Marquez leads Andrea Dovizioso by 16 points in the overall season standings.
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