Bongo (73) died in a Spanish clinic on Sunday after ruling his country since 1967.
"President Bongo was a friend in his endeavours to strengthen and consolidate political and people to people relations between South Africa and Gabon particularly after the 1994 democratic dispensation in our country," Zuma said in a statement.
"President Omar Bongo has contributed enormously to the African continent through his involvement in peaceful resolution of conflict in the central African region and the continent as a whole.
"On behalf of the government and the people of South Africa and on my own behalf I wish to express our heartfelt condolences to the people of Gabon and President Bongo's family during these trying moments.
"Our thoughts and prayers go out to the family that also lost a mother and a first lady only three months ago," Zuma said.
Edith Lucie Bongo Ondimba (45) who was a trained paediatrician and an HIV-Aids activist, died in Morocco in March.
She was the eldest daughter of President Denis Sassou Nguesso, of the Republic of Congo.
A video of a boy being forced by his parents to run almost naked in the snow has sparked an uproar.
Cosatu met with the Public Protector to discuss its numerous complaints against Premier Helen Zille.
Marine ruins have been discovered by builders working at the V&A Waterfront in Cape Town.
