Fatima Patel and Safydeen Aslam Del Vecchio also face charges of robbery and theft after they went on a spending spree using the couples' credit cards, building up a stash of jewellery, camping equipment and electronic devices which were found at a remote location where an ISIS flag was being flown.
The Hawks declined to provide any further information due to the sensitive nature of the case as the search continues for the couple whose vehicle was found abandoned more than 300 km away from where they were last seen on February 9.
But the weekly Sunday Times, quoting a charge sheet after their court appearance, reported that Patel and Del Vecchio also stand accused of contravening the Protection of Constitutional Democracy Against Terrorism and Related Activities Act by hoisting an ISIS flag at a modest homestead in a rural area.
Del Vecchio also faces another terrorism-related charge for allegedly participating in "extremist web forums that support ISIS and offering to supply phone numbers and sim cards that are not traceable."
Yousha Tayob, the lawyer representing Patel and Del Vecchio, confirmed that the pair had appeared in the court and were remanded in custody at Westville Prison in KwaZulu-Natal province.
Ebrahim Deen of the Afro-Middle East Centre told the weekly that South African Muslims posed no threat to travellers and that the incident was more related to crime than an ISIS attack.
"Muslims are largely integrated in (South African) society, are not disillusioned and they face little discrimination like in Europe and elsewhere," he said.
Martin Ewi of the Institute for Security Studies said South Africa was regarded as a "logistics base" for terror cells in transit, and is not traditionally a target for attacks, although the arrests of Patel and Del Vecchio confirmed the presence of an active terror cell in South Africa.
"We in the counter terror fraternity suspected that they were working as members of an active cell, and the kidnapping will confirm the presence of an active IS cell," Mr Ewi said.