"We as a country fully take responsibility for the death of your children. But we don't regret sending them," Mapisa-Nqakula told the mourning families of deceased soldiers on Thursday after their remains were repatriated at the Waterkloof military airbase.
Thirteen South African soldiers were killed and 27 injured during a skirmish with Seleka rebels this past weekend.
The South African National Defence Force troops were deployed to the country in 2007 as part of a bilateral agreement to train the Central African Republic military.
But on Thursday the Mail & Guardian reported how the SANDF were deployed to protect business interests related to the ANC as well as prop up the regime of deposed CAR president Francois Bozize.
Mapisa-Nqakula dismissed reports the soldiers were in CAR defending the business interests of politically connected individuals.
"They fought protecting South African interests. They were not protecting any business. There was a bilateral agreement signed that they were fulfilling," she added.
The minister also paid homage to the fallen soldiers' fighting efforts.
"To the mothers and fathers, I can only imagine what you're going through. I've never lost a child," she said. "They were all very young, but they were lions. They fought with honour."
She encouraged families to remember the soldiers were not forced to be deployed to the CAR.
"Painful as it may be, know that your children died fighting. I say this in all sincerity, without any arrogance," she added.
"This was not the first deployment and it won't be the last. What is important now is to remember what your children stood for and that they died as heroes."
Deputy Defence Minister Thabang Makwetla visited the surviving soldiers in One Military Hospital after the repatriation ceremony.
"You inspire us to work harder to do more," Makwetla told Warrant Officer Zwelithini Nkosi.
"You've served your country and we are forever grateful for that."
The 48-year-old Nkosi suffered a distressed fracture on his right femur from a bullet wound during battle.
"This wound is nothing. We were doing our job," he said.