British Airways and kulula.com flights are back in the air on Thursday morning.
This comes after the South African Aviation Authority reinstated its air operations certificate following a five day suspension citing safety concerns.
The operator says its schedules will be restored in a phased manner.
Customers are advised to check whether their flights are reinstated before going to the airport.
Last week saw passengers stranded and with no choice but to book with other airlines, most of which applied hefty price increases on their tickets.