The bodies of Darcey-Helen, two, and Chloe-Ann, one, were discovered in a car outside their home near Brisbane in 31C (87.8F) heat.
Their mother, Kerri-Ann Conley, 27, was arrested on Saturday night.
She is the first person to be charged under Queensland state’s expanded definition of murder, which includes reckless indifference to human life.
9 News reports Ms Conley rushed the girls inside and attempted to cool them down after finding them inside the car.
Paramedics and police were called but they declared the children dead at the scene.
Witnesses told local media they had seen officers carrying the girls, who appeared to be soaking wet.
One woman told The Sunday Mail: “The police were carrying the girls out… their shirts were ripped open like they’d tried to save them.”
Neighbour Willow Dawes told the Courier Mail she was there when the ambulance arrived and the children were brought out.
“It’s pretty upsetting and it was quite confronting,” she said.
Queensland Police Detective Inspector Mark White said the children appeared to have been “exposed to extreme heat”.
“We are speaking the parents of those children. It’s a very tragic incident which has occurred,” he said.
Tributes to the girls, including teddies and flowers, have been left outside their home.
The family were known to the Department of Child Safety and an investigation is under way, according to Queensland State Premier Annastacia Palaszczuk.
Ms Conley was also charged with possession of drugs.
The Australian reports that police are investigating whether drugs had played a role in the incident.
Ms Conley will appear at Beenleigh Magistrates Court on 11 December.
