South Africa has asked Taiwan to move its de facto embassy out of its administrative capital, Pretoria.
It has given Taipei six months to relocate its liaison office to the commercial hub of Johannesburg.
The decision is seen as highlighting Beijing's expanding sway among developing nations.
While Taipei has accused Pretoria of bowing to pressure from China, Beijing has welcomed the decision.
"The One China principle is the political foundation for China to establish and develop diplomatic relations with countries. It is also a widely recognized norm in international relations," said China's Foreign Ministry spokesperson, Mao Ning
"We appreciate South Africa's correct decision to relocate the Taipei liaison office out of its administrative capital, Pretoria. Taiwan independence is unpopular and doomed to failure," she said.
China opened its embassy in South Africa in 1998, a year after Pretoria severed formal diplomatic ties with Taiwan over which Beijing claims sovereignty.
However, like many countries, South Africa has maintained unofficial diplomatic relationship with Taiwan.
This latest move comes at a time of heightened tensions between Beijing and Taipei.
Taiwan marked its national day last week and has repeatedly China's claims of sovereignty.
Days later, China held its latest round of military drills around Taiwan.
China is South Africa's largest trading partner globally, and one with which it is looking to expand cooperation.
Both countries are part of the BRICS bloc of developing economies which will hold its annual summit in Russia next week.
