The South African Civil Aviation Authority (SACAA) had grounded Comair's planes indefinitely on Sunday for unresolved safety issues, suspending its air operator certificate and stranding hundreds of passengers.
"After a thorough review of Comair's documentation, the SACAA has lifted the precautionary suspension of Comair's licence," Chief Executive Glenn Orsmond said in a statement late on Wednesday.
"We're pleased that the situation is finally resolved."
The airline aims to restore normal operations as soon as possible to assist customers, he added.
As flight schedules are to be restored in a phased manner, customers are advised to check them on the airlines' website before going to the airport, Comair said, while it would contact those with existing reservations.
In its notice on Saturday, the regulator pointed to Comair's safety problems in the past month, ranging from engine failures and malfunctions to landing gear malfunctions, among others.
The regulator said its investigation turned up three findings that "pose an immediate risk" to be tackled immediately.
Comair said no safety and security findings were made on flight operations or maintenance, adding that the regulator's findings related to quality assurance, the structure and personnel of the safety department and repair documentation.
Comair's suspension took out 40% of market capacity, prompting competition authorities to warn other airlines against price gouging after complaints of large price increases.
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