Katiza Cebekhulu, once a close associate of President Nelson Mandela's former wife, claims that in 1989 he watched her stab Stompie twice after accusing him of spying. He claims Jerry Richardson, the captain of Mrs Mandela's infamous Mandela United Football team, which terrorised Soweto in the late 1980s, restrained the boy.
Mr Richardson was jailed for life for Stompie's murder after a trial in 1991. Mrs Mandela, who denied the murder, was found guilty of kidnapping Stompie. A six-year jail sentence was later commuted to a R15000 (pounds 2,000) fine.
"Winnie had something sharp in her hand," Mr Cebekhulu claims in journalist Fred Bridgland's new book, Katiza's Journey. Beneath the Surface of South Africa's Shame. "I cannot say whether it was a knife or a pair of scissors ... I saw how she lifted her arm twice and stabbed Stompie twice. I could not see whether she hit him on the neck or on the chest."
The book also claims that the former white South African government and the African National Congress covered up Mrs Mandela's involvement to prevent it endangering the talks which led to a peaceful transition to democracy.
The book's allegations, which are the subject of a BBC television Inside Story Special tonight, add to growing pressure on the President's former wife - who now also uses her maiden name and calls herself Mrs Madikizela- Mandela - about a case which has in recent months come back to haunt her.
She has been supoenaed to appear later this month before the Truth and Reconciliation Commission to answer questions about the activities of her bodyguards. The case is extremely politically sensitive. Mrs Mandela still has huge grassroots support despite her divorce and currently chairs the ANC Women's League.
Mr Cebekhulu, who surfaced in a Zambian jail after disappearing from South Africa and is currently in London under the wing of former MP Emma Nicholson, has applied to the Truth and Reconciliation Commission for amnesty for apartheid-era crimes. The Commission, charged with exposing the truth about the apartheid era, has the power to grant amnesty in return for full confessions.
According to the Johannesburg Mail and Guardian Mr Cebekulu, in his affidavit to the Commission, has confessed to taking part in another murder ordered by Winnie Mandela. He claims he drove two men to the house of Dr Abu-Bakr Asvat, a Soweto GP, who is believed to have examined Stompie before the boy was murdered.
The two men - Thulani Dlamini and Cyril Mbatha - were later convicted of the doctor's murder and claimed robbery was their motivation. But the Mail and Guardian claims the men have now alleged from prison that Mrs Mandela contracted them to kill the doctor to cover up Stompie's murder. The doctor died four weeks after Stompie was found lying in a ditch with his throat cut.
The Commission said last week that Mrs Mandela would be questioned about the doctor's death. Commission officials have also said that she will also be asked about the disappearance of other Soweto children.
Mrs Mandela has claimed that she is being persecuted. She says she will refuse the Commission's offer to give evidence in private and appear publicly as she has nothing to hide.
Ms Nicholson will meet the Commission in Cape Town as the book is being launched. She has power of attorney over Mr Cebekhulu's affairs.