A statement from the South African Foreign Ministry confirmed that "His Holiness the Dalai Lama" had provided written confirmation of the cancellation of his planned visit.
This came after South Africa had failed to provide any formal response to his visa application.
"We have informally received contact His Holiness won't get his visa," said Nangsa Chodon, the Dalai Lama's representative in South Africa.
The Tibetan leader, who won the Nobel Peace Prize in 1989, had planned to attend a meeting of other laureates next month in Cape Town.
In 2011, he was prevented from travelling to South Africa to attend the 80th birthday of his friend Desmond Tutu, the former Anglican Archbishop of Cape Town. And in 2009, he was denied permission to attend a peace conference.
Patricia de Lille, the mayor of Cape Town and an opponent of the ruling African National Congress party, said that South Africa would suffer "international humiliation" if it barred the Dalai Lama.
In 2012, China was South Africa's biggest bilateral trading partner, with imports and exports of 300 billion rand ($33.7 billion).