Zuma commended Tutu on Tuesday, saying: "The archbishop has been a tireless and visible ambassador of our country all over the world, promoting human rights and justice."
The Unesco/Bilbao human rights prize was established in 2008 after an endowment from the city of Bilboa in Spain, and is given to institutions or individuals, who have significantly contributed to a culture of human rights at a regional and international level.
Zuma's good wishes came as a surprise as Tutu has often publically criticised the president and the ANC.
Tutu has been vocal on Zuma’s corruption charges, his involvement in the arms deal and the government’s refusal to allow the Dalai Lama a visa to South Africa.
In 2011, Tutu commented with regards to Zuma’s corruption charges; “I am very fond of President Zuma ... but I do believe it would have been better for him to have been pronounced innocent by a court of law weighing the evidence, rather than through a dubious administrator act."
The archbishop expressed outrage when Tibetan spiritual leader the Dalai Lama was denied a visa to South Africa, stating that the South African government "is worse than the apartheid government, because at least you were expecting it from the apartheid government".
Tutu stated that those who supported South Africa in its struggle against apartheid are "weeping" at the government's discourtesy to the Dalai Lama..