"Tendulkar has informed the Indian board and they have in turn told the Asian Cricket Council (ACC)," Asian team selector and former India opener Chetan Chauhan told reporters on Monday.
Tendulkar hit two centuries in India's 1-0 Test series win in Bangladesh on Sunday and was named the player of the series.
Compatriot Sourav Ganguly will replace him in the Asia squad for the three one-dayers against an Africa XI on June 6 in Bangalore and in Chennai on June 9 and 10.
Pakistan strike bowler Shoaib Akhtar and Sri Lankan pace duo Chamida Vaas and Lasith Malinga have already pulled out of the series created to raise funds for the Asian and African boards.
India's Zaheer Khan would replace fellow left-arm paceman Vaas and Sri Lankan Farveez Maharoof would come in for Malinga, Chauhan added.