The father's family insist he was trying to protect his children before the fatal incident, with a court hearing the mother had threatened their sons.
The 24-year-old man had been accused of driving a Mazda also carrying the mother and two sons that crashed into bushland south of Brisbane early on Saturday.
He allegedly fled the scene with a one-year-old son, leaving the mother behind with their injured three-year-old.
A witness took the mother and the boy to Beenleigh Police Station where officers attempted CPR, but the three-year-old died in the foyer after suffering head injuries in the crash.
The father was charged with breach of bail and contravening domestic violence orders.
He has not been charged over the fatal crash, with the incident still under police investigation.
The distraught father wept openly before he was denied bail at Southport Magistrates Court on Monday.
His legal team accepted their client was in breach of domestic violence orders but claimed the mother had instigated contact and threatened to harm the couple's kids before the crash.
The mother and children had travelled from the Gold Coast earlier in the morning and collected the father from a Beenleigh address before the crash, police have said.
"There is obviously a dispute in relation to facts relating to these charges," the father's Legal Aid lawyers told the court.
"From the material before the court, it is agreed by both parties that she approached him.
"His instructions are that the aggrieved (woman) was making threats toward the children, and he felt obliged to enter the vehicle."
The boy's mother claimed her former partner was armed with a gun, but the court was told investigators found no evidence of a weapon.
Outside court, family members claimed the boy's father was "forever innocent".
"We are sick of the f***ing lies," the boy's grandfather yelled at the media.
"He loves his kids ... he was trying to protect them. He would never hurt them."
Police are appealing for witnesses, with previous domestic violence incidents between the parents set to be central to the investigation.
A temporary protection order had been in place since June 2024 and the couple were separated, Detective Acting Superintendent Mark Mooney told reporters on Sunday.
A GoFundMe campaign to help pay for the boy's funeral had raised almost $5000 by Monday afternoon.
The father was remanded in custody for mention in Beenleigh Magistrates Court on November 19.
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