The Spaniard set a best time of two minutes 00.234 seconds on his final lap to claim his sixth pole of the season and take the top slot ahead of compatriot and championship leader Jorge Lorenzo on a Yamaha.
Marquez had set a record lap of 2:00.564 earlier in the session.
Marquez's team mate Dani Pedrosa completed an all-Spanish front row for Sunday's race with Italian Valentino Rossi, Lorenzo's team mate who is level on points with the overall leader but behind on race wins, qualifying fourth.
Marquez is 52 points adrift of Lorenzo and Rossi with seven races remaining.
Bradley Smith was the top British rider in qualifying, starting sixth for the non-works Tech3 Yamaha team with Honda-riding compatriots Scott Redding and Cal Crutchlow seventh and eighth.
(Reporting by Alan Baldwin, editing by Clare Fallon)
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