South African Airways (SAA) general manager for commercial Theunis Potgieter said the airline was reviewing its options.
"We would like to assure our valuable clients of SAA's long-term commitment to the Australian market," Potgieter said.
Qantas said it was disappointed by the decision.
"We believe the code share arrangements are of benefit to the public," Qantas said. The IASC report noted that while the Competition Commission of South Africa had allowed SAA to continue with the code-share arrangements until December 31, it also expressed apprehension regarding any further extension.
In its decision, the IASC said there were marginal competitive benefits from approving the code share in the short-term.
Any competitive benefits were uncertain and possibly negative in the long-term, it said.
"The continued existence of the code share agreement discourages entry and discourages competition between partner airlines from gateway cities other than Sydney and Perth," the IASC said.
SAA flies from Perth to Johannesburg, while Qantas operates from Sydney to Johannesburg.
Under their alliance, both carriers were required to operate a minimum of 10 services a week between Australia and South Africa.
- AAP