The 21-year-old Honda rider, who sealed a second straight title in Japan last week, matched the feat of Australian greats Mick Doohan and Casey Stoner when he scorched around the track in one minute 28.408 seconds in qualifying practice.
Briton Cal Crutchlow (1.28.642) was second fastest to put Ducati on the front row of the grid for the first time this year with Spain's Jorge Lorenzo (1.28.650) in third place for Yamaha.
"I'm really happy because we didn't start the weekend very well," Marquez told Speed TV.
"We will try and enjoy the race because this is our time to enjoy."
Marquez's brother Alex boosted his chances of taking another step towards his first world title when he clinched pole for Sunday's Moto3 race while Australian Jack Miller, who trails the Honda rider by 25 points, could only manage eighth on his KTM.
Tito Rabat could secure another world title for Spain first, though, and he took pole in the Moto2 race, where a win with anything worse than third place for his team mate Mika Kallio would make him champion. Finn Kallio will start in third place.
(Writing by Nick Mulvenney in Sydney, editing by Amlan Chakraborty)
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