The company had declared a force majeure at its Richards Bay Bulk Terminal - located off the Richards Bay port - late Friday after a second fire in a week hit operations at the port.
The cause of the fire is still not known, but no casualties were reported.
It did not clarify if the force majeure was still in effect or if exports had been affected.
"In Richards Bay, significant progress has been made in restoring operations - five of the seven conveyor belts have been fully restored and are back in operation," the country's monopoly freight and logistics firm said in a statement to its bondholders.
The port, which has Africa's largest coal export facility, has deployed manual handling to ensure continuity of operations to make up for the conveyor belts that were still un-operational, it added.
The company's Durban grain export terminal was also hit by a fire on 16 October, Transnet's statement said.
Out of the two conveyor belts at the Durban port, the one handling grain was affected by the fire.
"The terminal is working around the clock to ensure that the belt is restored and back in operation by the time the next grain vessel arrives at the Port on 26 October 2021," the company said.
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