The Italian set a new pole record of one minute and 44.502 seconds at the Twin Ring Motegi circuit as he put Ducati at the front of the grid for the first time since Casey Stoner at Valencia in 2010.
Yamaha's Valentino Rossi placed second and Dani Pedrosa was third in front of his Honda teammate Marquez, whose bid to wrap up the title with three races to spare has been hindered by glitches.
The 21-year-old Spaniard, who had a minor crash after a brake malfunction on Friday, had to pull off the track and switch to a new bike during yesterday’s practice.
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