Siyabonga Cwele announced Mo Shaik's appointment Friday.
Shaik served in the underground intelligence of the apartheid-era African National Congress which was headed by Zuma.
Shaik has served the government in several intelligence and diplomatic positions.
His brother Schabir, a former business adviser of Zuma, was found guilty of bribery and fraud in 2005. Zuma was implicated in the corruption case and it nearly stymied his chances of being president.
The main opposition party criticized the appointment, saying it was inappropriate and that he was "hopelessly partisan."