The LevelUp MTA rider set a 1:34.056s on his sixth lap of Phillip Island, securing a career-first at his home race.
Spain’s Jose Antonio Rueda was second for Red Bull KTM Ajo, just 0.091s in arrears of Kelso.
Luca Lunetta completed the front row for SIC58 Squadra Corse on the leading Honda, 0.225s off the pace.
Kelso was aided by a tow from his teammate Matteo Bertelle, who qualified fifth behind Taiyo Furusato.
Kelso said he was inspired by fellow Australian rider Jack Miller, who earlier in the day qualified third.
“I saw Miller chuck it on the front row before so I had to follow it up for the Aussies out there and get pole,” said Kelso.
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“Ready to rumble tomorrow. I think we’re in the best conditions. To be honest, mate. These are the best conditions you get for Phillip Island.
“And to be honest, even this morning I wanted that lap record, so today in qualifying I knew I had to really send it out there to get that lap record and obviously pole.
“Me and my teammate did some good work together, getting the slip stream down the main straight.
“It’s what I needed, just that little bit extra one or two tenths that helps. It was a helluva lot easier.”
Australia’s other interest, Jacob Roulstone, was 13th on the other Red Bull KTM Ajo with a 1:34.979s to be 0.923s off the pace of his compatriot Kelso.
New Zealand’s Cormac Buchanan was 17th for Denssi Racing BOE.
Sunday’s Moto3 race gets underway at 12pm AEDT.
Results: Moto3 Australian Motorcycle Grand Prix, Phillip Island (Q2)
| Pos | Num | Rider | Team | Bike | Lap | Gap | Diff |
| 1 | 66 | Joel Kelso | LEVELUP-MTA | KTM | 1:34.056 | ||
| 2 | 99 | Jose Antonio Rueda | Red Bull KTM Ajo | KTM | 1:34.147 | 0.091 | 0.091 |
| 3 | 58 | Luca Lunetta | SIC58 Squadra Corse | Honda | 1:34.281 | 0.134 | 0.225 |
| 4 | 72 | Taiyo Furusato | Honda Team Asia | Honda | 1:34.406 | 0.125 | 0.35 |
| 5 | 18 | Matteo Bertelle | LEVELUP-MTA | KTM | 1:34.447 | 0.041 | 0.391 |
| 6 | 83 | Alvaro Carpe | Red Bull KTM Ajo | KTM | 1:34.492 | 0.045 | 0.436 |
| 7 | 78 | Joel Esteban | CFMOTO Gaviota Aspar Team | KTM | 1:34.563 | 0.071 | 0.507 |
| 8 | 31 | Adrian Fernandez | Leopard Racing | Honda | 1:34.584 | 0.021 | 0.528 |
| 9 | 28 | Maximo Quiles | CFMOTO Gaviota Aspar Team | KTM | 1:34.703 | 0.119 | 0.647 |
| 10 | 94 | Guido Pini | LIQUI MOLY Dynavolt Intact GP | KTM | 1:34.870 | 0.167 | 0.814 |
| 11 | 82 | Stefano Nepa | SIC58 Squadra Corse | Honda | 1:34.880 | 0.01 | 0.824 |
| 12 | 95 | Marco Morelli | GRYD – Mlav Racing | Honda | 1:34.906 | 0.026 | 0.85 |
| 13 | 12 | Jacob Roulstone | Red Bull KTM Tech3 | KTM | 1:34.979 | 0.073 | 0.923 |
| 14 | 36 | Angel Piqueras | FRINSA – MT Helmets – MSI | KTM | 1:35.000 | 0.021 | 0.944 |
| 15 | 10 | Nicola Carraro | Rivacold Snipers Team | Honda | 1:35.010 | 0.01 | 0.954 |
| 16 | 6 | Ryusei Yamanaka | FRINSA – MT Helmets – MSI | KTM | 1:35.033 | 0.023 | 0.977 |
| 17 | 14 | Cormac Buchanan | DENSSI Racing – BOE | KTM | 1:35.140 | 0.107 | 1.084 |
| 18 | 22 | David Almansa | Leopard Racing | Honda | 1:35.454 | 0.314 | 1.398 |
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