Mr Kathrada's foundation announced that he died after being admitted to hospital with blood clotting in his brain earlier in March.
"With our brothers and sisters in South Africa, I mourn the loss of a liberator, and an exemplary leader", he said.
"We are deeply saddened to learn this morning of the passing on of our dear friend and founding trustee, Ahmed Kathrada", read a statement by the Nelson Mandela Foundation.
Following decades of activism, Kathrada was sentenced to life imprisonment and hard labour in 1964, together with seven other ANC luminaries such as Mandela, Walter Sisulu and Govan Mbeki, after a guilty verdict during the Rivonia treason trail.
The deputy leader of Congress in Rajya Sabha said Kathrada, known as Kathy, spent over 26 years in prison, and was resolute in fighting for freedom and justice for the oppressed people of South Africa.
Unlike many struggle veterans, Kathrada, who was imprisoned on Robben Island, never held public political office after the fall of apartheid and Mandela's election as president in 1994. "He was a determined revolutionary who gave his entire life to the liberation struggle in our country", Hanekom said.
"May Ahmed rest in peace and rise in glory", Desmond Tutu, the former Cape Town Archbishop, said on Facebook. While he was in prison he was awarded four honorary doctorates.
Kathrada's close friend, Denis Goldberg and Andrew Mlangeni are the only two Rivonia Trialists still alive.
Kathrada was politically active until his death, criticising the direction in which his beloved African National Congress was moving.
Apartheid was a legalised system of discrimination against non-white people introduced in South Africa in 1948.
The commemoration for Kathrada was attended by high profile figures‚ including former Speaker of Parliament Frene Ginwala‚ human rights lawyer George Bizos and political activist Sophie de Bruyn.
"We must do everything to ensure that the values which inspired him to battle, germinate a million times over and produce more of his calibre who will, instead of submitting, vigorously prosecute the struggle for a South Africa that truly belongs to all who live in it".
Deputy President Cyril Ramaphosa visited Kathrada's wife, Barbara Hoganâ€Ü at their home in Johannesburg to personally pass condolences to the family on behalf of the Government.
In recent years, Kathrada was a fierce critic of the ANC government under President Jacob Zuma, himself a fellow Robben Island inmate.
Kathrada will have an Islamic burial on Wednesday, the foundation said, while the government ordered national flags to be flown at half-mast.