Russia will be represented by its Foreign Minister Sergei Lavrov instead, the presidency said in a statement.
South Africa faced a dilemma in hosting the summit because, as a member of the International Criminal Court (ICC), it would theoretically be required to arrest Putin for alleged war crimes if he were to attend.
The ICC has issued an arrest warrant for Putin.
The leaders of Brazil, India, China and South Africa will attend the summit, the presidency said.