Nkurunziza, aged 55, died at a hospital in the Burundian capital on Tuesday.
Ramaphosa, who is also the African Union chairperson, expressed sincere condolences in a message to the government and people of Burundi at the loss of their leader.
“Burundi and all of Africa have lost a leader who was devoted to people-centred sustainable development, self-reliance, the sovereignty of his people and country as well as peace on the continent,” Ramaphosa said.
“It was under the leadership of President Nkurunziza that Burundi became one of the major troop contributing countries in the African Union Mission in Somalia. Burundi also deployed troops in the Central African Republic," the president said.
Ramaphosa lauded the sound bilateral relations between Pretoria and Bujumbura, under which South Africa played a key role in the AU-led Burundi Peace Process which led to the signing of the Arusha Peace Accords in 2000.
Nkurunziza paid a State Visit to South Africa in November 2014, where the two leaders signed accords covering the setting up of a Joint Commission of Cooperation (JCC), cultural cooperation and a decision to establish a Joint Business Council.
Ramaphosa appealed to Burundians to maintain peace and calm following Nkurunziza’s passing, and in the aftermath of the recently concluded presidential, legislative and municipal elections.