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.
"We are estimating a loss of over 1 billion rand ($127 million) for the agriculture, forestry and fisheries sector," she said.
"Our members have returned to work," said George Strauss, President of the United Transport and Allied Trade Union.
"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.
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.
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.
