"China highly appreciates South Africa for its respect and support for China's sovereignty and territorial integrity," Foreign Ministry spokesman Qin Gang said at a daily news briefing.
Qin said that China firmly opposes the Dalai Lama's "secessionist activities" in any name.
"The Dalai Lama is a political exile who has been engaged, under the cloak of religion, in impairing China's sovereignty and territorial integrity as well as the unity of the Chinese nation," he said.
An aide to the Dalai Lama had yesterday said that the Tibetan spiritual leader cancelled a trip to South Africa for World Summit of Nobel Peace Laureates next month as Pretoria denied him a visa, fearing that his trip would jeopardise relations with China, a major trading partner.
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The summit, an annual gathering, is being held in Cape Town for the first time, with the arrangements being made by a local organising committee formed by foundations representing four South African peace laureates -- Anglican Archbishop Desmond Tutu, Nelson Mandela, FW de Klerk and Albert Luthuli.
Beijing is South Africa's biggest single trading partner, with two-way trade worth USD 21 billion in 2012. Both countries also cooperate in the BRICS grouping of emerging economies along with Brazil, India and Russia.
China regularly uses its economic and political might to put pressure on governments around the world to prevent contacts with him.
Beijing brands the Dalai Lama, who fled into exile in India in 1959 after an abortive uprising against Chinese rule of Tibet, a separatist.