After the initial round of voting, only Mahamat and Kenya's Foreign Minister Amina Mohamed were left to contest the position, with Mahamat eventually emerging victorious.
The results were informally announced in the halls of the African Union (AU) headquarters in Addis Ababa, Ethiopia, shortly before 5pm East Africa time.
A loyal ally of President Idriss Deby from the same Zaghawa ethnic group, the 56-year-old has held a number of senior Chadian posts, including prime minister (2003-05), before being named foreign minister in 2008.
Addis Abba - The foreign minister of Chad Moussa Faki Mahamat will be replacing African Union Commission chairwoman Dr Nkosazana Dlamini Zuma.
Mahamat replaces South Africa's Nkosazana Dlamini-Zuma who was elected to the post in 2012.
Other issues being discussed at the summit include whether to approve the re-admission of Morocco.
However, King Mohammed VI has been making diplomatic efforts over the previous year to try to win Rabat's readmission. She will be returning to South Africa in April after a handover period. Neither has said explicitly it will oppose Morocco's re-entry.
Conversely, Nigeria, Botswana and other states say the Hague-based court is an important legal backstop for countries whose domestic justice systems have been compromised by civil conflict.