The crash happened in bushland north of the Gold Coast at 5am on Saturday.
Police expect to lay further charges against a 24-year-old man, who will appear in court on Monday.
The father allegedly fled the scene of the crash, along with a one-year-old boy.
A witness saw the car veer off the road and later transported a 22-year-old woman and a three-year-old boy to Beenleigh Police Station.
Detective Acting Superintendent Mark Mooney said a temporary protection order had been in place since June 2024 and the couple had been separated.
"The three-year-old has sustained a head injury which has caused his death," Detective Acting Supt Mooney told reporters.
"Any previous domestic violence incidents that have occurred between the two (parents) will form part of our inquiries."
The child became unresponsive in the foyer of the police station and officers performed CPR, but the boy died.
Detective Acting Supt Mooney praised the efforts of officers who valiantly tried to revive the boy.
He said the mother had requested the witness to take her to the police station after the crash.
The 24-year-old man from Beenleigh was believed to have been the driver of the vehicle.
Police found the man and the toddler at an address in Beenleigh around 90 minutes after the incident.
The boy was taken to the hospital for observation. Both adults were also checked over at the hospital before being medically discharged.
The police investigation is continuing.
Officers have appealed for further witnesses to come forward.
1800 RESPECT (1800 737 732)
Lifeline 13 11 14
Men's Referral Service 1300 766 491
14°C