Qualifying was delayed by 30 minutes, after another round of rain arrived in the early stages of fourth practice on Saturday, causing a lengthy red flag in that session.
However the second phase ended up being the driest session of the weekend so far, with a downpour scheduled to arrive during the 15 minutes failing to do so.
Marquez rolled the dice to run slick tyres, while factory Yamaha riders Jorge Lorenzo and Valentino Rossi struggled and will start 12th and 15th at Phillip Island on Sunday.
Australian Grand Prix
Marquez hones cricketing skills ahead of Australian GP
21/10/2016 AT 06:05
Rain was expected halfway through Q2, and with a dry line having emerged through the first phase in which riders favoured intermediates, Marquez headed straight back to the Honda garage after his initial outlap to change to slicks tyres.
He emerged five minutes into the session, and was unstoppable for the remainder.
Marquez's first flying lap was a 1m32.239s and fastest by 0.851 seconds, and while he was quickly eclipsed by Cal Crutchlow, his next lap was a 1m30.670s and 1.519s clear.
That prompted other riders to try either a slick rear of two slick tyres, but they couldn't get close to the Spaniard.
With 30 seconds remaining, Marquez went faster again with a 1m30.189s that was a neat 2.000s ahead.
LCR Honda's Crutchlow - who progressed from Q1 after topping that session by 1.985s - changed to a slick rear for his final run and improved again to a 1m30.981s to secure second on the grid with his last lap.
In the end, Marquez's advantage for his sixth pole position of the season was a still-sizeable 0.792s.
Marc VDS Honda's Jack Miller was third when the chequered flag was shown, but was bumped down by Pol Espargaro and Aleix Espargaro, the Tech3 Yamaha pilot 0.566s faster than his Suzuki-riding brother.
Still, fifth for Miller is the Australian's highest MotoGP qualifying result, eclipsing his previous best of 12th, while Pramac Ducati's Danilo Petrucci completes the second row of the grid.
Nicky Hayden qualified seventh on his return to the factory Honda garage standing in for Dani Pedrosa, ahead of Aprilia's Stefan Bradl and Ducati pair Andrea Dovizioso and Hector Barbera.
Both Yamaha riders had to contest the first phase of qualifying for the first time since the format was introduced in 2013, after - like Crutchlow - missing the best conditions in FP3.
Lorenzo made it through to Q2 with second in Q1, as the circuit dried rapidly, but he could only manage 12th in the main session, 8.651s slower than Marquez despite switching to slick front and rear tyres.
Rossi gambled on an intermediate rear tyre at the end of Q1 but did not have enough time to get it up to temperature.
He failed to advance and 15th is his worst qualifying result since lining up 17th for the 2011 Aragon GP.
Incoming Yamaha rider Maverick Vinales could only manage third in Q1, three tenths behind Lorenzo on his Suzuki, and he will start 13th.
Bradley Smith occupied the second place set to progress through to Q2 with 90s to go, but he crashed at Turn 8 and fell to qualify between Vinales and Rossi, while Yonny Hernanez looked an outside chance to pip Lorenzo on his final lap before crashing at Turn 10.

Grand Prix Australia MOTOGP qualification results

1. Marc Marquez (Spain) Honda 1:30.189
2. Cal Crutchlow (Britain) Honda 1:30.981
3. Pol Espargaro (Spain) Yamaha 1:31.107
4. Aleix Espargaro (Spain) Suzuki 1:31.673
5. Jack Miller (Australia) Honda 1:31.754
6. Danilo Petrucci (Italy) Ducati 1:32.420
7. Nicky Hayden (U.S.) Honda 1:32.944
8. Stefan Bradl (Germany) Aprilia 1:33.015
9. Andrea Dovizioso (Italy) Ducati 1:33.090
10. Hector Barbera (Spain) Ducati 1:33.914
Grand Prix Valencia
'An inspiration for me' - Federer leads Rossi tributes after final race
14/11/2021 AT 17:23
Motorcycling
Rossi announces decision to retire at end of season
05/08/2021 AT 14:45