Morbidelli posted a fastest lap time of one minute 30.191 seconds and will start from the front of the grid, ahead of Jack Miller of Pramac Racing.
Honda's Takaaki Nakagami will begin Sunday's race from third on the grid, his third successive front row start.
Championship leader Joan Mir, who will clinch the title with a podium finish on Sunday, will start from 12th, one spot behind contender Fabio Quartararo of Yamaha.
Alex Rins' title aspirations were dealt a blow as he failed to make it into the second qualifying session.
Seven-times premier class champion Valentino Rossi of Yamaha, who was cleared to race this weekend after a COVID-19 scare, will start from 16th on the grid. (Reporting by Arvind Sriram in Bengaluru)