The girl was found in a sweaty state with matted hair by staff from a nearby bottle shop.
There was no evidence of any food or water and only one of the windows had been left ajar.
It's understood that the man's older daughter was meant to be looking after the five-year-old but after an argument ensued between the pair, she got out of the car and walked away.
Instead of waiting for his daughter to return, the man then entered the establishment, leaving his youngest daughter, who suffers a host of medical issues, all alone.
Appearing at Blackwater Magistrates Court, the man took full responsibility for his actions and plead guilty to leaving a child under 12 unattended.
His solicitor Zoe Craven told the court that he was a full-time carer for his daughter and often travelled throughout the state to take her to nutritionists and specialists.
'He wasn't thinking clearly at the time and was operating under stress,' she said.
'For the most part he has been a very caring and attentive father to his child,' she added.
Magistrate Robert Walker said that a jail sentence would be appropriate given the seriousness of the offence, but after taking into consideration the man's role as a single father and full-time carer, he placed the man on 18 months probation.
A conviction will also be recorded for the offence.