The 21-year-old Spaniard, who last week sealed his second successive world title, steered his Repsol Honda around the course in one minute 28.408 seconds.
That was almost a quarter of a second quicker than second-placed Cal Crutchlow as the Briton, riding for Ducati, held off Jorge Lorenzo, who completed the front row for Movistar Yamaha.
Victory would be Marquez’s 12th of the season, which would set a new MotoGP record, while he has two races remaining to go past Casey Stoner and clinch the pole record outright.
He said: “We expect a hard-fought race (on Sunday), but I just have to enjoy it. Above all, it will be difficult to stop both Jorge and Valentino (Rossi), who seem to have the fastest race pace.
“My focus and ambition are the same as ever and we will try to be at the front, but also over the weekend we have been trying different things out with next season in mind.”
Lorenzo’s team-mate Rossi, joint second in the standings, will start on the third row after qualifying eighth. He is level on points with Dani Pedrosa, Marquez’s team-mate, who will start fifth, while Lorenzo is three points further back over the season.