Zuma said the nation’s thoughts and prayers were with the deputy president’s family.
“I wish to convey, on behalf of government and the people of South Africa, our deepest words of condolence. May her soul rest in peace,” Zuma said in a statement.
The African National Congress on also voiced words of comfort to the family. ANC spokesman Jackson Mthembu said the party had learnt with sadness about the passing away of Masefako Sophia Motlanthe.
“The passing of Mrs Motlanthe, while not unexpected as she was of advanced age, is a loss not only to the Motlanthe family. It is a loss to the ANC family and indeed the entire South African society.”
She died of natural causes at her home in Meadowlands, Soweto, on Friday, aged 89.
A memorial service would be held on Thursday, and the funeral on Saturday.
She died a day before Motlanthe’s wedding to long-term partner Gugu Mtshali in Houghton, Johannesburg.