Some movement of cargo impacted.
The state-owned company already suffered major disruptions to its ports and national freight rail line last week following days of unrest and violence in parts of the country.
In response to a question on whether the cyber attack on Transnet was linked to the unrest, a government official said: “We are investigating, and when that is confirmed or dispelled we are going to make that announcement.
“Currently we are treating it as an unrelated event.”
The latest disruption has delayed containers and auto parts, but commodities were mostly unaffected as they were in a different part of the port, one of the sources said.
It will also create backlogs that could take time to clear.
Transnet said its container terminals were disrupted while its freight rail, pipeline, engineering and property divisions reported normal activity.
Most of the copper and cobalt mined in the Democratic Republic of Congo and Zambia, where miners such as Glencore and Barrick Gold operate, use Durban to ship cargo out of Africa.