The Durban port has suffered major disruption after days of unrest, and operations have also been badly affected at the Richards Bay port and on a national freight rail line, logistics and freight companies said on Wednesday.
Violence erupted last week in KwaZulu-Natal after the jailing of former president Jacob Zuma, but it has rapidly escalated in widespread looting and destruction in several other provinces.
Durban has one of the busiest shipping terminals on the African continent, and is a hub for exports including agricultural commodities and imports like crude oil and petroleum products. Richards Bay is home to a major coal export terminal.
State logistics group Transnet said in a statement that service levels at Durban and Richards Bay were impacted "as the entire supply chain is closed", including roads into and out of the ports.
The South African Association of Freight Forwarders told Reuters that port health services at Durban had been closed, effectively preventing vessels from berthing because Covid-19 testing could not be carried out.
"This situation is exacerbated by launch crews also not being available," it said.
Juan Enslin, managing director at the Leschaco Group, said his logistics firm had to leave several containers at the Durban port for safety reasons.
"We therefore will fall way behind in our delivery schedules. Cargo that has been on the road was also diverted," he said.
On the impact on freight rail, Transnet said force majeure had been declared on the Natal Corridor (Natcor) rail line that connects Durban to Gauteng - which is home to the country's financial and economic powerhouse, Johannesburg.
Force majeure allows certain terms of an otherwise legally binding agreement to be waived owing to unavoidable circumstances.
Transnet said it was deploying resources to avert commercial fuel operations being affected, after being served with a force majeure notice by the Sapref oil refinery.