"She has driven to work and parked her car without knowing he was in there," police said.
"The boy's mother located him in the vehicle and he was conveyed to hospital where he remains in a stable condition. Police are treating the incident as an accident."
The boy was treated overnight at the Royal Children's Hospital. It has been confirmed the boy was the son of a staff member at the nearby Newport Gardens Primary School.
The school is about 100 metres from where the boy was located.
An Education Department spokesman said they were providing support to the boy's family, students and teachers.
Temperatures in Melbourne yesterday soared above 30C, hitting 32C around 3pm.
But the temperature inside a vehicle can heat up to more than double the outside air temperature within minutes.
In summer, it can be up to 30C hotter than outside.
Police, paramedics and fire brigade crews had all rushed to the scene but police said they did not need to break into the car to reach the boy.
Nearby residents told the Herald Sun they did not recognise the Kia or know whether the boy's family lived in the street.
"It's just a very sad situation," one said.
"I can't imagine what the parents would be going through. It's sad whichever way it happened - especially when kids are involved."
Local detectives were called in to investigate, assisted by the homicide squad, who were notifed in accordance with police protocol. Police are treating the incident as an accident.
The youngster is a pupil at St Margaret Mary's Catholic Primary School in Spotswood, in Melbourne's inner west, where children are being offered counselling.
The boy's school is less than 4km from where he was found on Maddox Rd, Newport.
Catholic Education Melbourne executive director Stephen Elder said support was being offered to students and staff at the boy's school.
"Counselling is being made available to students and staff at St Margaret Mary's Spotswood after an incident yesterday when a member of the school family was found in a car," he said.
"Our thoughts and prayers are with the family of the child and the school community."
Ambulance Victoria figures show an average of four children a day are left to swelter in hot cars.