The 120,000 barrel-per-day (bpd) Engen refinery in Durban, majority-owned by Malaysia's Petronas, ceased operations as investigations started into the cause of the fire on Friday. Engen said it was taking measures to ensure security of supply.
The refinery shutdown comes at a crucial time for South Africa as it looks to kickstart an economy walloped by the COVID-19 pandemic.
The South African Petroleum Industry Association (SAPIA) warned in May that the country was facing a diesel shortage due to a spike in demand as restrictions on movement eased.
Africa's most advanced economy is a net importer of crude oil and petroleum products, with the local market consuming 11,142 million litres of petrol and 12,539 million litres of diesel in 2018, according to the SAPIA.
In July, the country's third-biggest crude refinery, Astron Energy's 100,000 bpd plant, was hit by an explosion that killed two people and injured several others. The plant remains out of commission.
(Reporting by Wendell Roelf; Editing by Pravin Char)