The man allegedly stole a Volkswagen from a supermarket car park on Maude St just before 2pm on Friday, November 14.
He allegedly removed the sleeping toddler from the car, placing the boy in a box in the car park before driving away.
The victim returned and found the toddler, who was not physically injured and still sleeping.
Police found the stolen car with a broken windscreen in Mooroopna parkland the next day.
Shepparton Crime Investigation Unit detectives and officers from the Shepparton Divisional Response Unit officers arrested a 32-year-old Mooroopna man in central Shepparton at about 2pm on Friday, November 21.
The man will be interviewed in relation to the incident and serious driving offences.
Shepparton Criminal Investigation Unit Detective Acting Sergeant Andrew Costello said the boy’s mother was in the shops for “a matter of moments” when she came out to find her car gone.
He urged people not to leave their children unattended in vehicles, but also said the incident was brief and he understood how it could happen.
“She's completely aware that she's made an error in judgment ... remorseful for having done it,” he said.
“She'll never do it again, and she'll probably never forgive herself either.”
Police thanked the public for providing information leading to his arrest.