Velvet Sky resumed flights on Friday at around 2.30pm, after delays in the morning, the Airports Company SA (Acsa) said.
"Velvet Sky's flight from OR Tambo International Airport departed for King Shaka International Airport at around 2.30pm on Friday. The flight was originally scheduled to depart at 6.20am," Acsa spokesman Solomon Makgale said.
"More flights are expected to depart this afternoon."
Velvet Sky spokesman Gary Webb said that on Thursday flights were delayed due to a dispute with a service provider.
He said the airline was in the process of changing service providers, and that this was not concluded in time to operate.
"We changed a major service provider and there was a lot of paperwork that took longer than we expected.... We are legal now, all the processes were completed," said Webb.
Velvet Sky flights were delayed by up to five hours on Friday morning --two hours longer than originally expected.
All flights were cancelled on Thursday.
The broad-based black economic empowerment company is based in Durban and flies between that city, Johannesburg, Cape Town and Polokwane.