Marquez, already eliminated from the championship race, topped the timeseheets with a scorching lap of one minute 28.364 seconds around Phillip Island's bucolic seaside circuit on a day of brilliant sunshine.
The Honda rider's best was more than three-tenths of a second quicker than Ducati's Andrea Iannone and Yamaha rider Lorenzo, who posted matching times in their final flying laps.
Rossi, 18 points ahead of team mate Lorenzo, his only challenger with three races left, will start a disappointing seventh on the grid, having failed to capitalise on perfect conditions after emerging from his garage late in the session.
Honda's Dani Pedrosa heads the second row alongside fifth fastest Briton Cal Crutchlow and sixth fastest Suzuki rider Maverick Vinales.
Wily Italian Rossi is chasing a record-equalling eighth premier class crown and will trust in his race smarts to secure enough points on Sunday to maintain a solid lead ahead of the penultimate stop at Malaysia next week.
Two-time champion Lorenzo, however, was fuming after the session after Iannone rode in his slipstream to match his best lap and sandwiched his Ducati between Marquez and the Yamaha rider on the front row.
"This time Andrea benefited a lot from my wheel," said Lorenzo. "I did my best."
Iannone thanked Lorenzo.
"Without Jorge for sure, yes, I improve -- but not at this big step," the Italian said.
Rookie Alex Rins claimed his third pole of the season in the Moto2 category, with the championship already claimed by Johann Zarco, who starts seventh on the grid.
Championship leader Danny Kent clocked the fastest time in Moto3 but was hit with a six-place grid penalty for riding slowly on the racing line during free practice, allowing Saxoprint RTG's John McPhee to take his first ever pole.
(Editing by Peter Rutherford/John O'Brien)
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