A 200-wagon coal train derailed on Thursday, shutting down the railway line that links mines to the Richards Bay export terminal, Transnet said.
The crew were unhurt in the incident in which 51 wagons derailed.
"The export line has been closed to allow engineers and maintenance crew to re-rail the wagons and repair the line. The closure will affect all commodities that are transported on the line, like coal and chrome," Transnet's freight rail unit said in a statement.
Coal loadings this month are on course to be their highest since at least 2015, buoyed by strong demand in Asia.
The country has loaded 7.95 million tons of coal in December so far, Refinitiv Eikon data showed, up from 5.3 million tons in November and 6.5 million a year earlier.
"There is no estimated time of reopening at this stage but the intention is to open the one line that was not badly damaged as soon as possible so as to allow the flow of trains," Transnet said.