Police authorities say Chikunga was travelling on a highway south of the nation’s most populous city, Johannesburg.
A statement released by the transport ministry said the tires on Chikunga’s car "were punctured by spikes, bringing the car to a stop enabling the criminals to rob the occupants of valuables."
The minister and her guards emerged from the ordeal "unharmed and safe," the statement added.
Police spokeswoman Athlenda Mathe said the robbers got away with personal belongings and two South African Police Service, SAPS pistols.
"A manhunt has since been launched following this unprecedented incident and to bring to book those responsible," Mathe said.
Involving a high-profile official with an armed security detail, the incident is striking even for South African standards. The country has long had a reputation for violent crime and is often described as one of the most dangerous in the world outside a war zone.
Police recorded more than 500 robberies and almost 70 murders a day in the country of 62 million people from April to June this year, according to official statistics.
Authorities have been accused of failing to ensure safety and secure justice for crime victims.
"The SAPS is committed to executing its mandate of protecting the executive of the country and community at large," Mathe said.
"VIP protection is one of the key priority areas for the SAPS and has been undertaken with excellence over the years," she added.