None of the girls, ranging in ages from 11 to 13 years, were harmed, the St. Paul Pioneer Press reported.
Police said three girls were found in the parking lot of a St. Paul department store and two others were found at a residence.
The five students of Seward Montessori School in South Minneapolis left school at Monday afternoon and their parents reported them missing later. Investigators said they thought the girls were trying to run away together.
Acting on a tip, family members found three of the girls -- Isabel Ward, 13; Gabriella Woods, 12; and Keneni Legese, 11 -- just before 9 p.m. Tuesday in the parking lot of a store near the Capitol.
A family member said the girls apparently were trying to get to Wisconsin but split up, the Pioneer Press said. It wasn't immediately clear why they wanted to go to Wisconsin.
The other girls -- Malina Long Crow, 12, and Alexandra O'Brien, 12 -- were found at a residence in on St. Paul's East side.
Tammy Nygaard, mother of Gabriella, told the Minneapolis Star Tribune she was happy and relieved that her daughter was home, but there would be consequences, too.
"There's going to be a little bit of grounding. She won't get her phone back. And there will be a little extra housework," Nygaard said.