Maverick Vinales ended up second, ahead of Johann Zarco and Andrea Iannone.
Marquez was unstoppable across the 15-minute Q2 session, constantly bouncing back to the top with each run.
In the end, it was his 1m28.386s that bagged him a dominant pole - more than 0.3-seconds clear of the field.
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Dovizoso went into qualifying on the back of a nasty fall at the Lukey Heights turn in FP4, and never looked like contending for a front-row start.
The Ducati rider couldn't even finish inside the top 10, ending up more than a second off the pace after failing to improve on his final run.
The early part of the session was dominated by a three-bike long train featuring Marquez, Iannone, and Jack Miller.
Running nose-to-tail, they broke into the 1m28s for the first time this weekend five minutes in, Marquez leading the way.

Marc Marquez of Spain and Repsol Honda Team looks during free practice for the 2017 MotoGP of Australia at Phillip Island Grand Prix Circuit on October 20, 2017 in Phillip Island, Australia

Image credit: Getty Images

Those times lasted until the final runs, when Zarco jumped to the top with a 1m28.744s.
He was then beaten by Vinales' effort of 1m28.719s, before Marquez trumped them all at the flag.
Miller's best time left him an impressive fifth - a career best - ahead of Pol Espargaro, who also took KTM's best grid spot.
Valentino Rossi came through Q1 to qualify seventh, followed by Aleix Espargaro and another Q1 runner, Bradley Smith.
Cal Crutchlow had been sitting seventh before the final sprint at the end of the session, and was set to improve with a little under three minutes to go sa he went fastest through sector one.
But he went down at the Honda corner, his session effectively over on the spot, and he'll start the race in 10th place.
Dani Pedrosa finished at the back of the queue, and will start from 12th.
Rossi topped the 15-minute Q1 segment of qualifying, while Smith secured passage to Q2 for the second time in as many rounds with second.
That meant Jorge Lorenzo missed out on a Q2 spot, going just sixth quickest in the wake of his FP3 crash, which left him with a suspected sprained ankle.
The Ducati rider will start the race from 16th.
Rossi went quick enough to top Q1 before the final flurry at the end of the session with a time of 1m20.665s set five minutes into the session, but still improved on his final run to put progression beyond doubt.
It wasn't quite as comfortable for Smith, but the KTM driver jumped from fifth to second on his final run to secure his third Q1 spot for the season, and second in succession.
Smith's late lap knocked Alex Rins out of Q1, the Suzuki rider falling just over a tenth short of progression.
Australian rider Broc Parkes, standing in for the ill Jonas Folger, did an impressive job on an unfamiliar Tech 3 Yamaha, out-pacing Alvaro Bautista and Sam Lowes to qualify 21st.
Starting grid
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