Roanan Ace was trapped in the Holden Barina for up to two hours in 35C heat in Maryborough, southeast Queensland, on Tuesday afternoon.
His parents woke up to find their son unconscious in the car, the Courier-Mail reports.
Paramedics were unable to revive Roanan and he was pronounced dead at Maryborough Hospital at 4pm.
Chris Foley, a local church pastor, is providing emotional support to the grieving parents, 38-year-old Danny and 29-year-old Christie Ace.
In a tragic twist, 19 years ago another three-year-old boy was accidentally killed when he ran in front of Mr Ace's motorbike.
"He actually came to me once and said he never fully understood what it must be like to lose a son until he had one of his own," Mr Foley was quoted as saying.
"That's why they're just so gutted ... They're going through hell and back."
Police say heat was the suspected cause of Roanan's death, but investigations were continuing.
Cabin temperatures can reportedly peak at more than 60C on days with 30C highs.