The woman, from Gladstone Park in the city's northwest, was released on bail and is due before Melbourne Magistrates' Court on January 23.
If the boy does not survive, the investigation could be transferred to the homicide squad, the Herald Sun reports.
Alison Connell, 58, who lives across the road from the pub told the newspaper: "My mum called me and said there's been a child left in a car and it's in a pretty bad way. I was horrified."
Temperatures in Melbourne reached 36C on Wednesday.
Tests previously run by Ambulance Victoria found even on a 29C day the inside of a car can reach 44C in 10 minutes and 60C within 20 minutes.
Kidsafe Victoria says leaving children unattended in a hot car, even for a short time, "can be fatal".
"Children are particularly at risk because they can lose fluid quickly, become dehydrated and suffer from heatstroke," the organisation states on its website.
"Every year in Australia, over 5000 children are rescued after being left unattended in a car."
It shared a video on Monday from Ambulance Victoria reminding people of the dangers of leaving children unattended in cars given the warm weather forecast across the state.
It poses the question: "You wouldn't leave your ice cream in a hot car. Would you leave a child? Hot cars kill."