Corlett "Lolo" Sono, 21, and 19-year-old Siboniso Anthony Shabalala, were among about 21,000 people killed in political violence during apartheid by agents of the white-minority regime or by fellow activists within black liberation groups.
The decision to press ahead with the exhumation was revealed in our sister newspaper the Sunday Herald back in December and it was carried out yesterday.
In 1997, Mr Sono's father told South Africa's Truth and Reconciliation Commission (TRC) – a body set up to investigate apartheid-era atrocities – that he last saw his son in a pick-up truck with Mrs Mandela.
He told the commission Mr Sono had been beaten up and Mrs Mandela told him his son was an apartheid spy.
In her testimony to the TRC, Mrs Mandela described the allegations as ridiculous and lunacy, and the judge dismissed the statement from Mr Sono's father, who is now dead.
In 2012 an investigator from South Africa's Missing Person's Unit found records and photographs taken by mortuary officials in 1988 of men who were identified by family members as Mr Sono and Mr Shabalala. The family then gave the go-ahead for the exhumation.
Madelaine Fullard, who runs the Missing Person's Unit, said: "Last year we found records of two young men who were brought to the mortuary after being stabbed many times and dumped in a field. Their bodies were not claimed and they were given a pauper's burial."
The mortuary where the records were kept and the graveyard where the men were buried are in the same district where Mr Sono and Mr Shabalala lived.
Ms Fullard added: "We are confident it is them but DNA and forensic tests will now be conducted so police can resume their investigation."
Once the face of resistance to white minority rule, Mrs Mandela – who was known as the Mother of the Nation and was elected rector of Glasgow University – fell from grace in the late 1980s.
She became more militant in her fight against apartheid and increasingly paranoid about activists turning traitor.
The TRC found Mrs Mandela, who is still an ANC MP, and her former security detail, known as the Mandela United Football Club, had killed 18 people in Soweto, the sprawling township that served as the epicentre of anti-apartheid resistance.
In 1991, she was convicted of kidnapping and assaulting a minor who later died. Her jail sentence was reduced to a fine the following year.
Caroline Sono, Lolo Sono's stepmother, campaigned unsuccessfully for more than two decades for Mrs Mandela – known as Ms Madikizela-Mandela since Nelson Mandela divorced her – to reveal her stepson's burial site.
Mrs Sono told the Sunday Herald: "If he is not buried [properly] his spirit is roaming around. We know justice is never done for people like us in South Africa, but in our society we have to bury our loved ones properly for there to be closure.
"We just want Lolo's bones so we can bury him properly and his spirit can be with us, and for Winnie to say she's sorry. She's not the Mother of the Nation, she's the killer of the nation."