"President Zuma is the Chinese people's old friend and good friend," Xi said as he welcomed Zuma on a state visit as trade and political ties between Pretoria and Beijing grow closer.
"South Africa is the comprehensive and strategic partner of China in Africa," said Xi, who visited South Africa in March 2013 as part of his first foreign trip as head of state.
"We are good friends and good brothers that mutually benefit each other."
"For me, this is a manifestation of the friendship and solidarity that exists between the People's Republic of China and the Republic of South Africa," Zuma said.
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China is South Africa's single largest trading partner, while South Africa is China's largest trading partner on the continent.
South Africa joined the BRICS bloc of developing economies with Brazil, Russia, India and China in 2011.
During the apartheid era, Zuma's African National Congress was supported by Moscow while Beijing backed the rival Pan Africanist Congress, but in recent years South Africa has maintained a strongly pro-China foreign policy.
Dozens of Nobel laureates boycotted a September meeting in Cape Town following the latest refusal, which was widely regarded as a sign of South Africa's deference to Beijing.
Fellow laureate and anti-apartheid activist Desmond Tutu also slammed the government over the visa refusal. The meeting was forced to moved to Rome.
During Zuma's visit, China announced the signing of a series of agreements, including a memorandum of understanding on nuclear energy cooperation between China National Nuclear Corporation and the South African Nuclear Energy Corporation.
Detailed terms of the agreements were not immediately available.