The DAMS driver was quick from the off, tackling torrential downpours before setting a 1m45.118s to top the timesheets for his first pole position since Abu Dhabi last season.
He went quickest at the halfway mark and despite being briefly demoted by ART driver Theo Pourchaire, reclaimed the top spot before a crash from third-placed Martins saw the session end three minutes early.
Home favourite Jack Doohan, who led the morning's practice session, was first out amid torrid conditions, telling his engineer that he was aquaplaning before adding "it is so bad".
By the time he had made it to the end of his first lap, the session had been stopped, with crashes throughout the field.
Ollie Bearman had a huge shunt into the wall along the back straight in his Prema-run car, the Briton smashing his front wing on the way to Turn 9, but was able to rejoin the session after the stoppage.
Fellow Ferrari Driver Academy member Arthur Leclerc (DAMS) had a spin at Turn 9, with Red Bull junior Jak Crawford (Hitech) losing a front wing.
After a 15-minute stoppage, the rain had somewhat subsided, and despite poor visibility, the session resumed.
Alpine Academy member Doohan set an early benchmark of 1m52.238s before Saudi Arabia feature race winner Frederik Vesti (Prema) surpassed him by two seconds.
Virtuosi's Doohan improved the next time around but was quickly toppled by Isack Hadjar (Hitech) as Martins slotted into second.
Iwasa took the lead at the halfway mark with a 1m46.376s, before Martins put in the first sub-1m46s lap to take the lead next, with a 1m45.736s.
Team-mate Pourchaire went quicker by 0.001s but Iwasa then shaved 0.6s off the Frenchman's time to assume the top spot prior to a crash from Martins at Turns 5 and 6 that curtailed the session.
Hadjar will line up fourth ahead of fellow rookie Zane Maloney (Rodin Carlin), with Bearman sixth.
Dennis Hauger will start on reverse-grid pole for Saturday's sprint race for MP Motorsport ahead of Kush Maini (Campos Racing) and Leclerc.
F2 Australia Qualifying Results
| Cla | Driver | Team | Time | Gap |
|---|---|---|---|---|
| 1 |
 Ayumu Iwasa |
 DAMS |
1'45.118 | |
| 2 |
Theo Pourchaire |
ART Grand Prix |
1'45.732 | 0.614 |
| 3 |
Victor Martins |
ART Grand Prix |
1'45.736 | 0.618 |
| 4 |
Isack Hadjar |
Hitech Pulse-Eight | 1'46.037 | 0.919 |
| 5 |
 Zane Maloney |
Rodin Carlin | 1'46.045 | 0.927 |
| 6 |
 Oliver Bearman |
 Prema Powerteam |
1'46.058 | 0.940 |
| 7 |
 Arthur Leclerc |
DAMS |
1'46.309 | 1.191 |
| 8 |
 Kush Maini |
 Campos Racing |
1'46.530 | 1.412 |
| 9 |
 Jak Crawford |
Hitech Pulse-Eight | 1'46.687 | 1.569 |
| 10 |
 Dennis Hauger |
 MP Motorsport |
1'46.737 | 1.619 |
| 11 |
 Ralph Boschung |
Campos Racing |
1'46.859 | 1.741 |
| 12 |
Jehan Daruvala |
MP Motorsport |
1'46.896 | 1.778 |
| 13 |
 Frederik Vesti |
Prema Powerteam |
1'46.899 | 1.781 |
| 14 |
 Roy Nissany |
PHM Racing by Charouz | 1'47.194 | 2.076 |
| 15 |
 Jack Doohan |
Invicta Virtuosi Racing | 1'47.266 | 2.148 |
| 16 |
 Enzo Fittipaldi |
Rodin Carlin | 1'47.267 | 2.149 |
| 17 |
 Roman Staněk |
Trident |
1'47.470 | 2.352 |
| 18 |
Richard Verschoor |
Van Amersfoort Racing |
1'47.533 | 2.415 |
| 19 |
Clement Novalak |
Trident |
1'47.578 | 2.460 |
| 20 |
Juan Manuel Correa |
Van Amersfoort Racing |
1'47.989 | 2.871 |
| 21 |
 Amaury Cordeel |
Invicta Virtuosi Racing | 1'48.198 | 3.080 |
| 22 |
Brad Benavides |
PHM Racing by Charouz | 1'50.122 | 5.004 |
| View full results | ||||
