The child died from head injuries after his father allegedly fled the scene with his one-year-old brother as the mother scrambled to save the toddler.
The fatal incident happened in bushland north of the Gold Coast at 5am on Saturday.
A witness saw the white Mazda veer off the road and crash.
The witness took the 22-year-old mother and the three-year-old to Beenleigh Police Station, where officers attempted CPR.
A temporary protection order had been in place since June 2024 and the couple had been separated, Detective Acting Superintendent Mark Mooney said
"The two adults have been in a relationship for a number of years, currently separated and the two children are their children," he confirmed to reporters.
The 24-year-old man is in custody charged with breaching a domestic violence order and police expect to lay further charges when he appears in court on Monday.
Det Acting Supt Mooney said any previous domestic violence incidents between the parents would form part of police inquiries.
He has appealed to the public to help, seeking any dashcam footage that might have captured the incident.
He praised the efforts of officers who valiantly tried to revive the boy.
"The toddler was unresponsive upon arrival, he was in a bad medical way ... and the three-year-old has sustained head injuries which has caused his death," Det Acting Supt Mooney said.
"We understand the mother and the two children had travelled from the Gold Coast earlier in the morning arriving at the Coral Street address (in Beenleigh) where they collected the male (father)."
Police found the man and the one-year-old at an address in Beenleigh about 90 minutes after the incident and the baby boy was taken to the hospital for observation.
The crash was a tragedy, Queensland Premier David Crisafulli said.
"My reflection on that incident is how traumatic it is for every single individual," he told reporters in Petrie on Sunday.
"For family, for first responders who were there, for the people who drive past, for every Queenslander who wants to see vulnerable people protected.
"They're the kinds of incidents that rock at the core of a state."
The 24-year-old man from Beenleigh was believed to have been the driver of the vehicle.
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