The Liqui Moly Dynavolt Intact GP rider will start from second with his teammate Manuel Gonzalez alongside in third.
Pole position went to Italtrans Racing Team rider Diogo Moreira, whose lap was only 0.011 ahead of Agius.
The Sydneysider said he still had time to find.
“Stoked to be on the front row,” said Agius.
“Now, reflecting on that lap, I made a couple of mistakes, especially to take the final corner.
“I missed it (pole position) by nothing. It would have been a dream first pole position.
“I’m stoked to be on the front row, but I’d be lying if I didn’t want the pole.”
As for Sunday’s race, Agius is optimistic about his chances.
“We’ll go for it,” he said.
“Our race pace is good. Still need to keep calm and work on a couple of things to be good tomorrow, but I can’t wait.”
Sunday afternoon’s Moto2 race is scheduled for 1:35pm AEDT.
Results: Moto2 Australian Motorcycle Grand Prix, Phillip Island (Q2)
| Pos | Num | Rider | Team | Bike | Lap | Diff | Gap |
| 1 | 10 | Diogo Moreira | Italtrans Racing Team | Kalex | 1:29.817 | ||
| 2 | 81 | Senna Agius | LIQUI MOLY Dynavolt Intact GP | Kalex | 1:29.828 | 0.011 | 0.011 |
| 3 | 18 | Manuel Gonzalez | LIQUI MOLY Dynavolt Intact GP | Kalex | 1:29.893 | 0.076 | 0.065 |
| 4 | 96 | Jake Dixon | ELF Marc VDS Racing Team | Boscoscuro | 1:29.993 | 0.176 | 0.1 |
| 5 | 27 | Daniel Holgado | CFMOTO Power Electronics Aspar Team | Kalex | 1:29.995 | 0.178 | 0.002 |
| 6 | 80 | David Alonso | CFMOTO Power Electronics Aspar Team | Kalex | 1:30.107 | 0.29 | 0.112 |
| 7 | 71 | Ayumu Sasaki | RW-Idrofoglia Racing GP | Kalex | 1:30.128 | 0.311 | 0.021 |
| 8 | 44 | Aron Canet | Fantic Racing | Kalex | 1:30.141 | 0.324 | 0.013 |
| 9 | 15 | Darryn Binder | ITALJET Gresini Moto2 | Kalex | 1:30.267 | 0.45 | 0.126 |
| 10 | 7 | Barry Baltus | Fantic Racing | Kalex | 1:30.327 | 0.51 | 0.06 |
| 11 | 75 | Albert Arenas | ITALJET Gresini Moto2 | Kalex | 1:30.382 | 0.565 | 0.055 |
| 12 | 14 | Tony Arbolino | BLU CRU Pramac Yamaha Moto2 | Boscoscuro | 1:30.382 | 0.565 | 0 |
| 13 | 99 | Adrian Huertas | Italtrans Racing Team | Kalex | 1:30.383 | 0.566 | 0.001 |
| 14 | 28 | Izan Guevara | BLU CRU Pramac Yamaha Moto2 | Boscoscuro | 1:30.504 | 0.687 | 0.121 |
| 15 | 95 | Collin Veijer | Red Bull KTM Ajo | Kalex | 1:30.536 | 0.719 | 0.032 |
| 16 | 64 | Mario Suryo Aji | Idemitsu Honda Team Asia | Kalex | 1:31.126 | 1.309 | 0.59 |
| 17 | 17 | Daniel Muñoz | Red Bull KTM Ajo | Kalex | 1:31.234 | 1.417 | 0.108 |
| 18 | 4 | Ivan Ortola | QJMOTOR – FRINSA – MSI | Boscoscuro | 1:33.703 | 3.886 | 2.469 |
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