Police confirmed to news.com.au the woman was working as the girls' au pair at the time.
Azzopardi was charged by detectives from the Bendigo Sexual Offences and Child Abuse Investigation Team with two counts of child stealing and stating a false name.
Detectives also charged the 31-year-old with handling stolen goods.
She was allegedly found with a passport and driver's licence in July that had been stolen from a Brighton East woman last year.
The alleged child thief, who police said is of no fixed address, was remanded in custody to appear in Bendigo Magistrates' Court tomorrow.
Sydney woman Samantha Azzopardi was charged in Canada. Photo / Calgary Police Service
Both girls were returned uninjured to their parents and the investigation is ongoing.
It was revealed in July that a couple from Brighton East in Melbourne's southeast claimed they were victims of fraud after hiring an au pair to look after their daughter for a year.
In a post on Facebook, they said a woman had told them her name was Harper Hernandez but they now believed she was "serial con artist" Samantha Azzopardi.
The family also alleged Azzopardi had run off with the mother's "identification documents".