Honda's Marquez was still three tenths of a second off Lorenzo's pace, with Yamaha's Italian great Valentino Rossi completing the front row of the starting grid in 1:30.128.
Lorenzo is moving to Ducati next season with Spaniard Maverick Vinales replacing him. The Suzuki rider was fourth fastest on Saturday.
Marquez's team mate Dani Pedrosa qualified eighth, a month after the Spaniard broke his collarbone, leg and foot in a crash in Japan.
"When I pushed a little bit in the second free practice and I did a one minute 30.4, I imagined going 1:29.9, 29.8 but not this 29.4, for sure," Lorenzo said.
"It’s unbelievable how far we can go when it’s time to make the perfect lap."
(Reporting by Alan Baldwin, editing by Ed Osmond)
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