Sidibe, 56, will start his new job as executive director of the UN AIDS program based in Geneva, Switzerland. He has served as UNAIDS deputy executive director since 2007.
His predecessor, Belgian Peter Piot, has headed UNAIDS since it was launched in 1995 and had previously indicated his intention to leave office at the end of his mandate in late December.
Ban announced his decision in Doha, on the margins of a high-level meeting on development financing, Ban's spokeswoman Marie Okabe said.
Before joining UNAIDS in 2001, Sidibe worked for 14 years at the United Nations Children's Fund (UNICEF).
On Friday, the United Nations urged countries to focus on the roots of the HIV/AIDS epidemic and draw on a panoply of tried-and-tested tools to prevent HIV from spreading among people most at risk.
"There is no single magic bullet for HIV prevention," Piot warned.