The two children, aged one and two, were found unresponsive by officers in Queensland on Saturday. It is unclear how long they had been inside the car.
The two girls showed evidence of being exposed to extreme heat, a police officer said.
Temperatures at the time they were discovered in the vehicle, in a town near Brisbane, were about 31C (88F).
Their mother, Kerri-Ann Conley, 27, is the first person to be charged with murder after Queensland state expanded the definition of murder to include "reckless indifference to human life".