The names of the South Africans snatched with 18 other people from the Malaysian resort near the southern Philippines are Karel and Monique Strydom from Johannesburg.
They are both 36 years old.
Department spokesperson Ronnie Mamoepa said that the couple's family had been informed about the kidnapping on Monday afternoon.
Mamoepa said South Africa's High Commission in Malaysia was involved in discussions with Interpol.
"The government is doing everything in its power to secure the release of these two people," he said.
Mamoepa confirmed that the kidnapping is believed to be political.
"Someone from the department is on the spot to liaise (with the Malaysian government)," Foreign Minister Nkosazana Dlamini-Zuma said at Johannesburg International Airport where she was waiting to meet Chinese president Jiang Zemin, who is due to start a state visit to South Africa on Monday. - Sapa