Velvet Sky was due to resume flight operations on Friday afternoon, after flight delays in the morning, the low-cost airline said.
"Our first flight for the day will take off at 1pm, and we are ready to fly," spokesman Gary Webb said.
"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."
Velvet Sky flights were delayed by up to five hours on Friday morning — two hours longer than originally expected.
On Thursday, Webb said the company was in a dispute with a service provider, and in the process of changing service providers, but this was not concluded in time to operate.
All flights were cancelled on Thursday.
The broad-based black economic empowerment company is based in Durban and flies between that city, Johannesburg, and Cape Town.
Velvet Sky said the delays, which started on Wednesday, were caused by circumstances beyond its control.