"We will always remember Tannie Ilse as the pillar beside her late husband, Dr Beyers Naude, a pioneer of non-racialism and one of the stalwarts of our struggle for liberation both here and abroad," said Zuma.
"They both loved and were loved by our people, black and white."
Ilse Naude, the wife of Afrikaner theologian and anti-apartheid activist Beyers Naude, died of a heart attack on Thursday.
She was 98.
Johan Naude, the eldest son of the couple, told Die Burger newspaper that were it not for his mother's strength, his father would never have achieved what he did in the fight against apartheid.
The couple were married for 64 years when Dr Naude died at the age of 89 in 2004.
The two met at Stellenbosch University where he studied theology and mathematics.
At his 80th birthday party former president Nelson Mandela praised the couple.
"His strength is of body and spirit and is the sort of power and indomitable spirit that beat the evil of apartheid and made him a hero of our people," Mandela said.
"If someone asks me what a new South African should be, I will say 'Look at Beyers and his wife, Ilse'."