Sindisiwe Chikunga told a parliamentary committee that one of the masked attackers pointed a gun at her head during the ordeal early on Monday.
They stole some laptops, a phone and her bodyguards’ weapons, she said.
South Africa has long faced high crime levels, including car hijackings, kidnapping and smash-and-grabs.
But it is very unusual for a government minister travelling with armed bodyguards to be robbed in their vehicle.
“I’m in one piece, but the whole experience was very traumatising,” Ms Chikunga told MPs.
She said that at 03:30 local time on Monday her bodyguards – or “protectors” – had got out of the car, which had been travelling on a main road south of Johannesburg, to replace a burst tyre.
That was when the robbers approached, forcing the bodyguards onto the floor and then opening the car door.
They “pointed a gun at my head and ordered me to come out”, Ms Chikunga said.
They demanded money, but she explained that she did not have any cash on her. They then searched through the vehicle taking what they could find.
Still waving their guns, the robbers also tried to take the minister’s ring but she told them: “This was the only thing that I have between my late husband and myself, I value it so much.”
The police have confirmed that the robbery took place and “a manhunt has since been launched following this unprecedented incident”, the AFP news agency reports.
In the latest annual survey nearly 1.3 million people said they had been victims of property crime.
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