Last week, Mrs Nomsa Tshabalala stood for hours in the late summer sun as workmen and forensic scientists dug seven feet down into the red earth of the local cemetery to begin bringing up the bodies.

One corpse, a bundle of dusty, brown bones in a white shroud in the mass paupers' grave, was that of her son Sibuniso Tshabalala, last heard of as a 19-year-old youth a quarter of a century earlier when he phoned his mother from the home of Mrs Winnie Mandela.

Tshabalala said: "He [Sibuniso] said: 'Mummy, I'm here with Lolo'. I said: 'Where are you?' but he dropped the phone and it went dead."

Nomsa Tshabalala, now old and frail, never saw or heard from her son again. But, according to witnesses at South Africa's post-apartheid Truth and Reconciliation Commission (TRC) and new evidence obtained by the Sunday Herald, Sibuniso and his close friend, Lolo Sono, were murdered within 24 hours of that phone call on the orders of Mrs Mandela, then the wife of Nelson Mandela.

Katiza Cebekhulu, a former member of Winnie Mandela's notorious vigilante gang, the so-called Mandela United Football Club (MUFC), has asserted to me in innumerable conversations that he saw the two youths being severely beaten in the garage of her home in Soweto, a sprawling black township to the southwest of Johannesburg.

Cebekhulu said Sono had already been severely beaten when he was taken, with a gun held to his head, in Mrs Mandela's blue minibus to her home. Mrs Mandela wielded a sjambok [whip] to beat both youths.

"Lolo was then beaten and kicked by football club members until he admitted that he worked with the [apartheid era] police," said Cebekhulu, who repeated his evidence publicly to the TRC.

Cebekhulu said Mrs Mandela ordered the execution of both youths when they were unable to produce documents she was seeking: "Winnie said, 'Take them away '. It was her order to kill."

They were "taken away" and never seen again. "I think Winnie needs to tell a court where she wanted Lolo Sono [and Sibuniso Tshabalala] taken away to," said Cebekhulu, who now lives in Britain. "I believe he was killed. He had been beaten really badly, so I don't think they would have taken him to hospital."

Mrs Mandela, who adopted the surname Madikizela-Mandela following her 1996 divorce from Nelson, may now be summoned to appear in court to explain how Sono and Tshabalala died. South African police last week opened a murder investigation into the deaths, and said they will take all information – including testimony from the TRC, which implicated Mrs Mandela in the youths' deaths – into consideration.

"The law must take its course," said Curtis Tshabalala, Sibuniso's younger brother, last week. "You can't kill someone's child and have it leave you like that. No-one is above the law."

The youths' corpses were exhumed from Soweto's Avalon cemetery following an exclusive report three months ago by the Sunday Herald that the bodies had been found. However, the country's ruling African National Congress (ANC) was blocking release of the news before a controversial leadership election on December 16, 2012. Riven by faction fighting and confronting issues of corruption, mass unemployment and eroding support, the party that has ruled for 19 years since the end of apartheid was appalled by the prospect of victims of Mrs Mandela and her football club rising from their graves during the conference.

The ANC warned parents of the dead youths that they must not talk to reporters, but late last year I managed to talk to two of them, who said they had been told by the National Prosecuting Authority (NPA) that the bodies had been found. They also confirmed the ANC threats.

The Sunday Herald revealed last December that the police and prosecuting authorities had known for a quarter of a century where the youths were buried and how they had been killed.

Last week, the NPA confessed that it had been in possession of a police docket relating to Sono and Tshabalala since one or two days after November 13, 1988, the date they "disappeared". Their bodies had been discovered on veld [grassland] beyond Soweto, said the docket. Photographs were taken of the bodies and put in the docket before they were tipped into the paupers' grave.

The docket subsequently "disappeared" for 25 years, like many others relating to alleged murders and other atrocities committed by the football club. When it was found, its photographic contents, clearly showing that the youths had been stabbed many times in their upper bodies, were presented to the Sono and Tshabalala families who confirmed they were of their missing relatives.

The ANC tried to orchestrate last week's exhumation for propaganda purposes, telling the parents what they could or could not say to the assembled press, and officials became irritated when the families declined to sing ANC liberation anthems: they sang hymns instead. John Sono, the uncle of one of the missing men, said: "We are closing the chapter of 'We don't know' and we are opening the next chapter beginning 'Here lies our son'." When a journalist asked if he wanted justice, Sono said, "That one is still very far. We still need to talk about it," before an ANC official shoved his hand in front of microphones, saying: "No, no, he can't answer that one."

Standing on the edge of grave number 2735, amid a profusion of late summer yellow veld flowers, Nomsa Tshabalala peered down at her son's skeleton and allowed herself a faint smile: "It has been 25 years since my child went missing, but I found him at last. I can finally have a life because I used to cry every day about my son. I believe I know how he died."

Asked who killed her son, she dropped her head sideways, away from the ANC officials, and whispered in Zulu, "It is Mama Winnie" before being ushered away by her family.

It is an allegation she has repeated to me many times down the years, and which she asserted at the 1997 TRC hearings.

Stompie Moeketsi is the best-known victim of the Mandela United Football Club. Katiza Cebekhulu and one of Winnie's drivers, the late John Morgan, accused her of stabbing the 14-year-old boy to death on New Year's Eve 1989, but she was convicted only of kidnapping and assaulting Stompie. She was sentenced to six years imprisonment, reduced on appeal to a fine of R5000 (£400).

South African forensic officers are now conducting DNA tests to prove beyond doubt that the remains are those of Sono and Tshabalala. The skeletons will then be airlifted to the United States and Bosnia where forensic anthropologists will try to assess exactly how they were killed.

Although the TRC felt unable to identify Madikizela-Mandela positively as the mind behind the Sono-Tshabalala killings, it did conclude that she was involved in their abduction and "finds therefore that Madikizela-Mandela must accept responsibility for the disappearances of Lolo Sono and Sibuniso Tshabalala". Both the TRC and the ANC denied Madikizela-Mandela's assertions that the youths were working with the apartheid police.

Last week's exhumations probably mark the end of Madikizela-Mandela's already fading political career. But new facts are emerging about the Stompie Moeketsi murder. In a new book I am completing with Katiza Cebekhulu, we question her alibi at the Stompie trial and report how the International Defence and Aid Fund (IDAF) was looted and finally destroyed to pay for her defence.

The London-based IDAF had, over four decades, raised about £100 million to provide legal aid and welfare to tens of thousands of South Africans, most of them black, accused of political offences under apartheid era laws.

The organisation that had smuggled huge sums of money into South Africa for the defence and aid of tens of thousands of anti-apartheid activists was closed down in 1991. Tragically, it had become more identified in the higher echelons of the ANC about the dispute over money for Winnie Mandela's defence than for what it had done on behalf of freedom fighters over many decades.