The four-day strike at Transnet widened on Wednesday after a second union joined the stoppage, the latest public protest ahead of next month's soccer World Cup tournament, being held in Africa for the first time.
The United Transport and Allied Trade Union (Utatu) and the South African Transport and Allied Workers Union (Satawu) represent 85 percent of Transnet's workforce of 54,000 people.
Utatu said it would stick to its 15 percent pay rise demand when talks reopen, above the 11 percent offered by Transnet.
"We will meet (Transnet's) management and the commissioner tomorrow (Friday). This could be the start to resolving the issue," Utatu General Secretary Chris de Vos told.
De Vos said Utatu and Satawu would meet the mediator from the Commission for Conciliation, Mediation and Arbitration on Thursday, and then all would meet Transnet on Friday.
Transnet said it was willing to discuss options other than a further wage raise to end the strike.
"It is not possible for Transnet to consider increasing the size of its offer, given that it would become unaffordable and unsustainable. We are going to have to look at other elements that have been negotiated in order to try find a settlement," Pradeep Maharaj, Transnet's HR Executive told.
Maharaj said 59 percent of the company's staff were participating in the strike, with the container sector in ports and its rail operations hardest hit so far.
"However, we are continuing to meet our critical requirements in terms of exports through the ports and movement of bulk commodities," he said.
Transnet does not operates passenger services, but a prolonged strike could affect imports, internal fuel supplies and exports of fresh fruit, grains, iron ore and coal.
South Africa is one of the world's biggest coal exporters, mainly to power stations in Europe and Asia.
The impact on coal and iron ore exports has been limited so far due to built-up stocks at ports, but the companies have said they would start feeling the crunch if the strike goes beyond this week.
In addition, miners said they were running out of space at the mines and would need to curtail production if they cannot ship their products to port.
Global miner Xstrata on Wednesday declared a force majeure, halting shipment of ferrochrome, a key ingredient in stainless steel, and chrome ore.
Samancor, the world's 2nd-biggest ferrochrome producer, also declared force majeure, traders said.
Transnet, and commodities and fuel producers said they would be able to supply customers for days due to stocks at ports.
Power utility Eskom said the strike at Transnet would have no impact on the transport of coal used to power its plants, since only small amounts were carried by rail, with the bulk supplied by conveyor belts from mines.
In a separate move, Satawu may strike over pay on Monday at the passenger transport service Metrorail, with Utatu expected to join, said Satawu's General Secretary Zenzo Mahlangu.
That strike would further hit the transport sector and could affect millions of commuters.
President Jacob Zuma late on Wednesday appealed to the striking workers to not disrupt the World Cup, and suggested they return to work for that period to make sure the tournament runs smoothly.