President Jacob Zuma has said he did not attend the funeral of a South African apartheid-era leader after Ahmed Kathrada's family asked him to stay away.

Kathrada died on Tuesday at the age of 87 after being admitted for surgery linked to blood clotting on the brain.

He was imprisoned for years along with Nelson Mandela for opposing the former white minority government.

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Kathrada last year called on President Zuma to step down after numerous corruption allegations.

The funeral attendees rose in a standing ovation when Kgalema Motlanthe, a former deputy president under Zuma, quoted from  Kathrada's letter urging the president to go.

There was another standing ovation for Finance Minister Pravin Gordhan, whose strong reputation as a bulwark against corruption has raised investor fears that President Zuma will soon fire him.

A statement from Zuma's office said the president would respect the wishes of Kathrada's family for him to stay away.

It also said South Africa "has lost one of its valuable and most respected freedom fighters".

Kathrada's coffin was covered in the flag of the ruling African National Congress party.

Mandela's ex-wife Winnie Madikizela Mandela, 80, attended the funeral.

Kathrada was born in 1929 to a scholarly Muslim family and became involved in political activism at the age of 11.

He and Mandela were part of a group sentenced to life imprisonment after the historic Rivonia trial of top ANC activists in 1964.

Kathrada was released from prison in 1989, just months before Mandela himself walked free.

During the past year, Kathrada was a regular at demonstrations and marches around South Africa, frequently offering his support to students protesting for free education.

In April last year, after South Africa's highest court found that President Zuma had violated his oath of office by refusing to abide by an order to pay back some of the millions of dollars in public money spent on upgrading his rural home, Kathrada wrote a letter to the president asking him to step down.

"Dear Comrade President, don't you think your continued stay as president will only serve to deepen the crisis of confidence in the government of the country," Kathrada wrote.

Kathrada was married to former government minister Barbara Hogan, who was sentenced to 10 years in jail for high treason against the apartheid government in 1982.