The two men were the first of 477 missing antiapartheid fighters who the National Prosecuting Authority -- whose investigations are modeled on the FBI -- was able to trace two years after being handed the cases by President Thabo Mbeki.
The Truth and Reconciliation Commission, which worked from 1995 to 2003 to shed light on abuses committed during the fight to overturn white-minority rule, had been unable to determine the fates of the 477.
Vusi Pikoli, director of the National Prosecuting Authority, pledged yesterday to find the others.
''This is the beginning of the process that will be able to restore the dignity . . . of those fighters for liberation who perished in the course of the struggle," he told relatives, antiapartheid fighters, government officials, and area residents gathered under canopies against the sun. ''We want to close this chapter of our history in South Africa."
Hundreds of people vanished as South Africa's then white rulers enforced their racist system through abductions, torture, and killings. Others died in clashes between security forces and guerrillas seeking to overthrow the regime.
Investigators used evidence presented to the Truth Commission and their own research to trace what was believed to be the graves of Ndaba and Maleka, if not all the details of how they died. DNA tests were being conducted on the remains to confirm the identities.
Investigators said yesterday that Ndaba, from the Pietermaritzburg area, and Maleka, from the black township of Soweto outside Johannesburg, were working for the armed wing of the now governing African National Congress when they died in a gun battle with security forces on April 13, 1988. The nature of their mission was unclear, and investigators did not learn exactly where they died.
Officials said security forces typically buried guerrillas killed in such clashes in unmarked paupers' graves.
''From here we are going to arrange the day of burying him properly," Ndaba's sister, Margaret Joe Ndaba, 68, said as she watched a team of forensic anthropologists from Argentina carefully clear the soil from the skeletons at the bottom of two gaping holes.
''What I'm glad about is that my brother is going to be buried like every other person," she said, adding that her brother did ''a wonderful thing" by dying for his country.
Ndaba left South Africa during the watershed student uprising of 1976 to join ANC guerrillas, but periodically made unannounced, usually brief, visits to his family. Then without explanation, the visits stopped. The family spent years trying to find out what happened to him. ''It was misery," his sister said, fighting back tears.
Maleka also joined ANC guerrillas in 1976. His mother, Joyce Sakoko Maleka, said police raids on her Soweto home were usually an indication he was back in the country on a mission. ''They came at night, kicked the doors, ransacked the house. But after these children are dead, we never saw these police again," she said.