The strike, in its third week, affected coal exports in one of the world's biggest suppliers of the power station feedstock to Europe and Asia. It may threaten the country's coal export target of 65 million tonnes this year.
The transport strike also dented exports of metals, cars, fruit and wine to Europe, as well as imports of vehicle parts and fuel, costing the economy at least 7 billion rand ($889.2 million) in lost production and sales.
The South African Transport and Allied Workers Union (Satawu) said a majority of its members had voted for Transnet's new offer, which included a one-off 1 percent payment on top of an 11 percent wage increase.
"The offer has been accepted ... and the understanding is that the workers will start going back to work tomorrow," Robert Mashego, Deputy President at Satawu, told Reuters.
The ruling African National Congress (ANC) had demanded a quick solution to the standoff, warning the dispute could hurt the World Cup, which runs for a month from June 11.
Satawu, which represents some 21,000 workers out of Transnet's 54,000 staff, had called for sympathy stoppages at other transport firms countrywide, including at the national airline and the coal export terminal. The stoppages could have begun next Tuesday if the Transnet dispute remained unresolved.
Recent strikes have drawn criticism from economists and the central bank, which say unions are trying to hold the government and state enterprises for ransom by staging strikes close to the World Cup, to squeeze pay hikes above inflation of 5.1 percent.
"We are seeing continued upside pressures on wages in both the public and private sectors," said Peter Attard Montalto, emerging market economist at Nomura International.
"Wage settlements are still unanchored from inflation and will cause a range of second-round inflation effects through the second half of the year ... leading ultimately to rate hikes."
Labour federation COSATU, which has nearly 2 million members and is a powerful ally of the ruling ANC, on Thursday threatened a strike during the World Cup over sharp power price increases by power utility Eskom if a mediation meeting planned for June 14 fails.
COSATU also said it may call a national strike from Oct. 7 if labour brokers, who provide contract workers to companies are not banned.
Late on Tuesday, South Africa's biggest union called off a strike at Eskom due to start on Wednesday after the state-owned firm obtained a last-minute court order declaring the planned industrial action illegal.
BILLION LOSSES
With a backlog that will take at least a month to clear, the strike has taken its toll on the country's mining, transport and manufacturing industries and hurt producers of perishable goods.
Transnet said that with 65 percent of its workers back on the job after the company's bigger union accepted a previous wage offer, the logistics group had managed to move a backlog of crucial shipments, including World Cup cargo and jet fuel.
