Matt McLean went deep at Dandenong Road with little more than a minute left in the two-part qualifying session to force an early end to qualifying for Race 1 of the weekend, Payne completing his lap just prior to officials drawing a halt to proceedings.
The split session saw the Super3 field out for the opening 10 minutes of the session, the circuit dry for the most part through damp patches remained in places.
As he'd done throughout Friday practice, Allen proved the pace-setter with a 1:12.5193s, improving to 1:12.1885s to sit 1.4s clear of second-best Brad Vaughan.
The Super3 session was halted with two minutes remaining when Blake Fardell got stuck on the slippery grass and mud after running off at Turn 1.
Following the restart, Vaughan improved to a 1:12.3134s, a mistake exiting the final chicane costing him.
It mattered little as Allen also went faster, logging a 1:11.9214s with a session best final sector.
The red flag was quickly shown when Elly Morrow spun at Turn 2, losing control over the kerb to spin, then becoming stranded as she recovered the car on the wet grass.
Just over six minutes remained as cars rolled back out after the restart, prompting something of a battle for track position.
Hill set to purple sectors to the back straight, converting that to provisional pole with a 1:11.1243s.
That put him ahead of Zak Best and Declan Fraser after their opening efforts, while a mistake from Angelo Mouzouris saw him run deep at Dandenong Round and tour the gravel.
Best improved on his second lap with a 1:10.8636s, only for Hill to also better his earlier effort with a 1:10.6791s to maintain his place at the top of the pile.
Payne rose to third with two minutes remaining, catching traffic in the final sector of the lap to bank a 1:10.8483s.
Best then usurped Hill once again with a 1:10.2692s before Everingham managed to go just 0.0054s faster.
Inside the final minute, McLean drew the red flag shortly after Payne had recorded 1:10.1828s.
Allen's Super3 best will see him start 14th in the 34-car field.