About one fifth of the 500-strong workforce at RBCT, the country's main export terminal for coal, went on strike last week after earlier rejecting the company's offer.
The workers were demanding a 10 percent pay rise.
"The strike is over ...the workers are back to work as of this morning and the terminal operations remained unaffected," RBCT spokeswoman Zama Luthuli said.
Africa biggest economy has been hit by a wave of industrial actions as well as threats of strikes that have led to above inflation settlements, stoking inflation fears.
South Africa's inflation rate slowed to 4.6 percent in May.
The transport sector was disrupted in May after workers at state-owned logistics group Transnet downed tools for three weeks in a work stoppage that cost Africa's biggest economy billions of rand in losses.
At the time, RBCT said South Africa was unlikely to reach its target of exporting 65 million tonnes of coal this year due to the strike that crippled rail and ports.
RBCT commissioned this year an expanded terminal to be able to handle up to 91 million tonnes of coal, but constraints on the rail line to the port are likely to cap exports at under 70 million tonnes for some years to come, analysts have said.
The port processed just over 61 million tonnes last year and in the first six months of this year the terminal shipped just under 28 million tonnes of coal, RBCT's data showed. Stocks at the end of June stood at 2.96 million tonnes.
Producers who export coal to Europe and Asia through RBCT include Anglo American's thermal coal unit, Xstrata, Optimum Coal, and South African diversified miners Exxaro and African Rainbow Minerals.
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