Israe, 15, and 16-year-old Louisa disappeared from their school in Haute-Savoie in the French Alps on Friday, prompting the police to launch a search for the pair.
The public prosecutor in Annecy said the teenagers "had left or were trying to leave for Syria".
"(They would) use any means possible to leave the country and were likely using fake identities," the police added.
The public prosecutor confirmed that both girls had returned home by Sunday evening - Louisa during the afternoon after hearing a TV appeal from her mother, and Israe a few hours later.
Israe was already known to authorities as "radicalized", and had been placed in foster care and banned from leaving the country.
A travel ban was put in place for Louisa on Saturday.
Israe's mother Nadia told Le Parisien newspaper that she had caught her daughter trying to leave for Syria two years ago.
"It is not easy to break this cycle... she has been sucked in by it," Nadia told the newspaper. "She wanted to go to Syria to help children and serve a good cause."
Following the incident, Nadia had alerted the authorities and Israe was enrolled in a deradicalization programme.
Dounia Bouzar, who runs the anti-radicalization centre Israe attended, said the 15-year-old had recently left a psychiatric hospital where she had been treated for "teenage depression". She described the teen as "fragile" and suicidal.
Louisa's uncle dismissed any allegations his niece was intent on travelling to Syria, describing her as simply a "runaway".
According to official sources, more than 1,000 French nationals, of which nearly a third are women, have travelled to Syria or Iraq to join the Islamic State group.
Almost 600 are believed to still be there and "at least 161" have died.