More than 3,000 workers -- including cabin crew, technical and ground staff -- started striking on Friday to demand higher pay and to protest against restructuring plans involving heavy job losses.
The walkout forced South Africa's cash-strapped flag carrier to cancel more than 300 domestic and regional flights between Friday and Monday.
South African Airways (SAA) said unions had agreed to start talks on Saturday mediated by an independent labour dispute resolution body.
"It is in the public interest that this dispute be resolved," said an SAA human resources manager Martin Kemp in a statement on Saturday, adding that the unions' "willingness to find a resolution" was "laudable".
Unions first threatened to strike after SAA announced this week that almost 1,000 employees could lose their jobs as part of a restructuring process.
Talks with management deadlocked after they failed to agree on wage hikes, prompting unions to press on with their threats.
SAA is offering a 5.9 percent pay rise, while unions are demanding an eight percent across-the-board hike and a three-year guarantee of job security.
"Our efforts are focused on finding solutions that accommodate the employee demands, safeguard the business and return operations to normal," said Kemp.
"We are exploring all possible avenues."
He added that it was a "critical time" for the company.
SAA is one of the biggest airlines in Africa. It employs more than 5,000 workers, with a fleet of more than 50 aircrafts providing dozens of domestic, regional and international flights each day.
But the carrier is deep in debt, despite several government bailouts, and has not posted a profit since 2011.
SAA spokesman Tlali Tlali told AFP the airline was losing 52 million rand ($3.5 million) per day due to flight cancellations.
International flights are scheduled to resume on Sunday, said the airline, while regional and domestic flights remain cancelled until Monday included.