The animals, also known as spectacled fruit bats, were unable to survive in temperatures which exceeded 42C.
In the city of Cairns, locals saw bats toppling from trees into backyards, swimming pools and other locations.
Wildlife rescuers found surviving animals clumped together, usually on branches closer to the ground.
"It was totally depressing," one rescuer, David White, told the BBC.
Last week, researchers from Western Sydney University finalised their conclusion that about 23,000 spectacled flying foxes died in the event on 26 and 27 November.
That tally was reached through counting by wildlife volunteers who visited seven flying fox camps following the heatwave.
Lead researcher Dr Justin Welbergen, an ecologist, believes the "biblical scale" of deaths could be even higher - as many as 30,000 - because some settlements had not been counted.