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.