The 24-year-old Spaniard, chasing his fourth MotoGP world title, leads Ducati rider Dovizioso by 11 points with 75 up for grabs in the last three races of the season.
Marquez swept around the 4.448 km Phillip Island track in one minute 28.386 seconds on his penultimate lap to knock Maverick Vinales off the top of the time sheets and claim his 44th career MotoGP pole.
"I was happy with the pace, happy more or less with the rhythm and now we wait to see what happens with the weather tomorrow," Marquez said.
Conditions were dry with blustery winds for the MotoGP riders on Saturday but some showers are forecast for race day on Sunday.
Vinales, third in the championship and 41 points behind Marquez, was second quickest in 1:28.719 and will line up on the front row along with fellow Yamaha rider, French rookie Johann Zarco (1:28.744).
Dovizioso, who beat Marquez in a thrilling wet race in Japan last week to breathe new life in the title race, slid off the track when he lost the front end of his bike at turn 10 in fourth practice earlier on Saturday.
The Italian walked away from the crash unscathed but never threatened the front-runners in the two qualifying sessions and will line-up on the fourth row just behind last year's race winner, British Honda rider Cal Crutchlow.
Australian Jack Miller, returning to race action only three weeks after breaking his leg, was fifth fastest on his Honda and will line up on the second row for his home race.
Andrea Iannone will lead off the second row for Suzuki with Spain's Pol Espargaro sixth fastest on the KTM, while Valentino Rossi, Aleix Espargaro and Bradley Smith will make up row three.
(Reporting by Nick Mulvenney in Sydney, editing by Peter Rutherford)
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