After seven rounds of voting, the Chadian foreign affairs minister defeated favourites Amina Mohamed of Kenya and Senegal's Abdoulaye Bathily.
He was a Prime Minister of Chad from June 24, 2003 to February 4, 2005.
Faki, a member of the ruling Patriotic Salvation Movement (MPS), has been Minister of Foreign Affairs since April 2008.
A total of five candidates vied for African Union Commission's post.
These are Dr. Amina Mohammed of Kenya, Dr. Pelonomi Venson-Moitoi of Botswana, Moussa Faki Mahamat of Chad, Agapito Mba Mokuy of Equatorial Guinea and Dr. Abdoulaye Bathily of Senegal.
The five Candidates conducted a public debate last month in Addis Ababa, Ethiopia.
Faki will receive the Chairpersonship from Dr Dlamini-Zuma, whose first term of office came to an end in June 2016, to lead the Commission for the coming four years.
Ghana’s Ambassador Thomas Kwesi Quartey was elected Deputy Chairperson.
Compiled by Amare Asrat