Marquez grabbed his 44th pole in his 88th MotoGP with a best lap time of one minute 28.386 seconds.
The Spanish Honda rider, who leads the world championship by 11 points with three rounds left, will start off on the inside of Sunday’s race grid from compatriot Maverick Vinales and French Yamaha racer Johann Zarco.
Andrea Iannone (Suzuki), Australian Jack Miller (Honda) and Pol Espargaro (KTM) will start off the second row of the grid.
Six-time race winner Valentino Rossi will join Aleix Espargaro (Aprilia) and Briton Bradley Smith (KTM) on the third row.
Andrea Dovizioso, who beat Marquez in a thrilling final lap duel in Japan last weekend, struggled in qualifying and will start off the fourth row along with last year’s race winner Cal Crutchlow and Dani Pedrosa.
Rossi and Smith advanced to the second qualifying session by finishing in the top two positions in the first session, for riders whose practice times were outside the top ten.
Rossi posted a best 1:29.346 lap time on his Yamaha, 0.359 seconds ahead of Smith on a KTM.
Triple world MotoGP champion Jorge Lorenzo, who injured his ankle in a tumble during third free practice, was sixth on his Ducati to push him down to 16th on Sunday’s race grid.