Xolile Mngeni, who was convicted of killing Anni Dewani while she was on her honeymoon, had been serving a life sentence for her murder.
His death comes amid the trial in Cape Town of British businessman Shrien Dewani, who denies arranging his wife’s murder.
Xolile Mngeni, 27, died in the hospital section of Cape Town prison, officials said.
South Africa’s correctional services department has said it will make a full statement about his death on October 18.
The death of Xolile Mngeni comes 12 days after Shrien Dewani went on trial.
Shrien Dewani, 34, faces five charges including murder and lying about the circumstances of his wife’s death.
He denies any involvement in the killing, which happened in the Gugulethu area of Cape Town.
Reports suggest prosecutors in South Africa had spoken to Xolile Mngeni but had not planned to call him as a witness in the trial because of the poor state of his health.
Xolile Mngeni was known to have had a rare brain tumor removed in 2011.
Anni Dewani was kidnapped at gunpoint and shot dead in Gugulethu, a township near Cape Town on 13 November 2010 while on honeymoon in South Africa. Shrien Dewani, who was kidnapped alongside her, was later released unharmed.
Xolile Mngeni was charged with murder, robbery with aggravating circumstances and kidnapping three days after her death and was convicted on November 19, 2012, of firing the shots that killed Anni Dewani, having denied the charges.
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