The 14 and 15-year-old schoolgirls ran away from Vienna and stayed the night with a friend in Graz, from where they planned to fly to Turkey and then cross the border into Syria.
However, the girl's mother became suspicious of the large amount of luggage the teenagers had with them and called the police on Saturday.
Police came to the apartment and were able to stop the two friends from boarding their flight.
Interior Ministry spokesman Alexander Marakovits said on Wednesday that one of the girls comes from a Muslim family, and the other is a convert. Both had been radicalised in the last few weeks and now wear a burqa, he said.
The Kronen Zeitung newspaper reported that the two girls got to know each other on the web and that one of them had said she wanted "to support Isis, it doesn't matter where".
"We are looking into how they were influenced, whether it be via the Internet or by actual people either in Austria or elsewhere," Marakovits said.
There was no evidence that their friend in Graz planned to fly with them to Turkey, as earlier media reports suggested.
Marakovits said that the girls are not being treated as criminals. "They are victims who have fallen in with the wrong circle of friends," he said. He added that they had been "lured with false promises" to Syria. They were promised a paradise and shown photos of beaches and beautiful homes. He said that they hadn't had any intentions of committing terrorist acts.
The parents' response had been right he said – they had registered their daughters as missing on Friday, and the information had been forwarded to all police stations.
Police have staff on alert at airports, to spot any minors attempting to fly to Turkey. A handful of young girls have already been prevented from leaving Austria for Syria.
In May two other Austrian girls of Bosnian origin reportedly left to "fight for Islam" in Syria.
The ministry spokesman said that 142 Austrians, including 12 women, were thought to be in Syria. Ten suspected would-be jihadis have been arrested in Austria since mid-August.