"We can confirm that she was leaving the country with the intention of joining IS, and she had been actively engaged with social media networks. Her parents have also confirmed she was using Twitter," said State Security Minister David Mahlobo.
The documents found in her room indicated that she was planning to join IS.
"The girl over the past period has been actually using technology, the social platforms, interacting with strange people and reading some material that suggested that she is actually getting an interest to join the terror group called ISIS," said Mahlobo.
The girl's grandparents found that she had escaped through a window from her locked room in Cape Town on Sunday morning.
The girl, who has not been identified as she is underage, has been returned to the custody of her family while authorities are investigating how she was able to buy a ticket and how it was funded.
The incident occurred amid growing concerns that IS militant group was recruiting in South Africa, although state security officials have repeatedly denied any knowledge of this.
In February this year, the Afrikaans daily Die Burger reported that they had confirmed details of a family in the coastal city of Port Elizabeth that had sold their home to go and join IS.
Professor Hussein Solomon, a lecturer in political science at the University of the Free State, earlier said that it was inevitable that there would be South Africans fighting for IS, as it had combatants from more than 60 countries.
Last year, Iraqi ambassador to South Africa Dr Hushaim al-Alawi said that three South African IS fighters were killed in Syria, with their deaths being covered up as car accidents.
Al-Alawi claimed that one of the many humanitarian assistance organisations in South Africa was being used as a cover for IS recruitment.

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