Being AFL Grand Final weekend, flights are predictably quite full.
I presume you're looking for the cheapest available price? Do you also prefer direct flight/s?
I'm looking at the outbound and inbound sectors separately. The cheapest flights from Perth to Melbourne are all overnight, unfortunately. But if that doesn't worry you, there is a Jetstar and also a Tiger flight leaving just after midnight on Wednesday 30/9, arriving Weds morning - both $299. There's also a Qantas flight leaving just before midnight Weds for $319, or a 6pm Tuesday departure to MEL, arriving Tuesday night for $275. There's also a Tigerair flight Wednesday afternoon for $329. If the other flights are too early, that might be your best bet otherwise I would go for the midnight QF flight.
Coming back it's a similar story but there are two semi-reasonably priced options for you on Monday. There is a 6.35am Virgin flight on Monday morning for $365. There's also a Tigerair flight in the evening for $369. Because there is a Jetstar flight departing 60 minutes later, you could use Jetstar's price beat guarantee to fly on Jetstar for $332.10 (10% off Tiger's price) by claiming it against the Tiger flight.