Police believe the girls hitchhiked or used public transport to cross into South Australia overnight on Thursday and provided false information at a checkpoint.
The girls, aged 15 and 16, were reported missing to Victorian authorities and were found on Friday morning after travelling to Goolwa, south of Adelaide, where they visited another girl.
All three had boarded a school bus to nearby Victor Harbor, with the bus stopped by police before it arrived at the local high school.
Police Commissioner Grant Stevens said the girls had since tested negative for COVID-19, eliminating the need for others on the bus or others they came into contact with to get tested or isolate.
He said after a proper assessment the appropriate judicial process would be followed and arrangements would be made to return them to their families in Victoria.
The commissioner said while authorities were more relaxed after the negative tests, the girls' behaviour had the potential to undermine all efforts put in place to protect South Australians from COVID-19.
"It's good that these two young girls have been found, it's very good that they have provided negative tests, but these sorts of activities do put us at risk," he said.
"The potential risk from these two young people, had they not been identified, is quite significant."
But Mr Stevens said it also had to be remembered that they were relatively young.
"Young people behave in a way that they might reflect on later in life and maybe regret," he said.
"You should keep it in mind that they are still children."
It remained unclear if the girls were from Melbourne or regional Victoria.
The incident came after SA had closed its border to Greater Melbourne in response to the city's latest coronavirus outbreak.
But it came before Friday afternoon's decision to also close the border to travellers from the rest of the state.
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