The Spaniard was joined on the front row for the 14th round of the season by compatriots Maverick Vinales, for Suzuki, and Yamaha's reigning champion Jorge Lorenzo.
Marquez's time of one minute 47.117 seconds was 0.631 faster than Vinales' best.
The top three all feature in the streak of eight winners but Ducati's Andrea Dovizioso, who has yet to win this season, qualified fourth ahead of LCR Honda's British rider Cal Crutchlow and Yamaha's Valentino Rossi.
The pole was the 64th of Marquez's career, equalling the record set by Lorenzo at the previous San Marino Grand Prix, and sixth of the season.
Former world champion Nicky Hayden of the United States, returning as a stand-in for injured Australian Jack Miller, qualified 19th and last but one on his non-works Marc VDS Honda.
With five races remaining, Marquez has 223 points to Rossi's 180 and Lorenzo's 162.
(Reporting by Alan Baldwin in London, editing by Ed Osmond)
