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".
She was also charged with possessing drugs and utensils or a pipe, ABC reports.
Queensland State Premier Annastacia Palaszczuk described the children's' deaths as "an absolute tragedy" and said the Department of Child Safety would review the case.
"I was heartbroken when I heard about it," she added.
She added the children were known to the Department of Child Safety.