The strike, now in its third week, has held up exports of metals, cars, fruit and wine to Europe and Asia, as well as imports of vehicle parts and fuel supplies three weeks before the World Cup starts.
South Africa hosts the World Cup in June and July, and football's world governing body FIFA said imports of some equipment for the event had been affected.
Jobs in agriculture were under threat, Minister of Agriculture, Fisheries and Forestry Tina Joemat-Pettersson told reporters.
"We are estimating a loss of over 1 billion rand ($127 million) for the agriculture, forestry and fisheries sector," she said.
So far, coal exports to power plants in Europe and Asia have continued thanks to stocks at the ports, and fuel supplies to petrol pumps are also as yet unaffected.
Strikers themselves are feeling the strain of lost wages.
"Our members have returned to work," said George Strauss, President of the United Transport and Allied Trade Union.
The smaller South African Transport and Allied Workers Union (Satawu), said its members remained fully behind the action.
"The strike is still on, none of our workers are back to work," said Zenzo Mahlangu, General Secretary at Satawu, which represents 39 percent of the 54,000 workers at Transnet.
Transnet said no meetings were planned with Satawu for Monday, but the rejected pay offer was still on the table.
More protests loom before the World Cup.
A strike by half of the workers at state-owned power utility Eskom, due to start on Wednesday, could disrupt electricity supplies and embarrass President Jacob Zuma's government before one of the world's premier sports events.
Civil servants, including nurses, police and teachers, may consider striking unless a mediator helps to resolve a wage dispute with the government.
The transport strike has hurt global miners with operations in South Africa, and carmakers warned they would shut their operations if it persists.
Anglo American Plc, Xstrata and the world's top steelmaker ArcelorMittal declared force majeure on the supply of iron ore, ferrochrome and steel. Transnet declared force majeure on coal destined for export.
