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As the coffin descended, a police bugler performed a rendition of The Last Post.
Meyiwa's wife wept, and appeared to be speaking to the slain Orlando Pirates goalkeeper as she threw a flower into the grave.
Meyiwa's father Samuel looked lost and forlorn, and seemed to be confused after being handed the South African flag that was draped over Meyiwa's coffin.
A heavy rain then began to fall.
As relatives approached the grave, they too began to weep.
Kaizer Chiefs players, led by goalkeeper Itumeleng Khune, placed flowers in the grave.
Mining magnate Patrice Motsepe, SA Football Association president Danny Jordaan and Deputy Agriculture Minister Bheki Cele also paid their respects.
Sports Minister Fikile Mbalula stood at the grave with a bowed head.
Meyiwa's grave was next to anti-apartheid journalist Nat Nakasa, who was buried at the cemetery in September, 49 years after he was buried in New York.
Meyiwa's former team-mate Andile Jali greeted Orlando Pirates chairman Irvin Khoza and Jordaan before going to speak to Meyiwa's parents.
A funeral service, attended by thousands of fans was held earlier at the Moses Mabhida Stadium in Durban.
Meyiwa was shot and killed on Sunday evening in Vosloorus, Ekurhuleni, while visiting his girlfriend, actress and singer Kelly Khumalo. Two men entered the house, demanding cellphones, and shot him before fleeing.
On Friday, a man appeared in court in connection with Meyiwa's murder.
Gauteng police spokesman Brigadier Neville Malila said: "[On Thursday], after receiving very positive information about a number of suspects, we conducted an identity parade during which some of the witnesses positively identified one person."
The 25-year-old Vosloorus resident, Zenokuhle Mbatha, was arrested and charged on the basis of the positive identification.
The National Prosecuting Authority said Mbatha would appear in the Boksburg Magistrate's Court again on November 11.
