The Honda rider, who sealed his third world title in Japan last weekend, took a gamble on slick tyres despite rain clouds looming overhead and was rewarded with a time of one minute, 30.189 seconds.
"I thought I'd take a risk because the track was completely dry," the Spaniard said after securing his 65th pole in grand prix racing.
"We will see if tomorrow if the race is dry because nobody knows about the tyres and nobody knows how to manage the race. We will do our best."
British rider Cal Crutchlow steered his Honda around the track in 1:30.981 to claim second place on the grid with Yamaha's Pol Espargaro rounding out the front row.
Spaniard Espargaro's late flying lap of 1:31.107 pushed his brother, Suzuki rider Alex, into fourth place ahead of Australia's Jack Miller and Italian Danilo Petrucci on a Ducati.
Heavy rain forced the cancellation of one of Friday's practice sessions and the red flag was out again during the fourth session after another downpour.
Yamaha's Jorge Lorenzo, last year's world champion, could manage only the 12th fastest time in final qualifying but at least he was involved in the session.
His team mate, seven-times champion Valentino Rossi, failed to reach Q2 for the first time since a new format was introduced in 2013. The Italian Yamaha rider will start 15th on the grid.
(Reporting by Nick Mulvenney in Sydney, editing by Peter Rutherford)
