The AU has 55 member states. Presidents or heads of government pick the commission’s leader, who is effectively the chief executive of the Addis Ababa-based secretariat running the AU.
Youssouf, who will serve a four-year term, replaces Moussa Faki of Chad, who has held the post since 2017.
The result is a blow for the high-profile Odinga, who sought support among allies at home and abroad.
The 80-year-old Odinga has sought Kenya's presidency five times over three decades, and the AU post would have been his last foray in public affairs. His long and colorful career in local politics peaked with his rise to the position of prime minister in 2008 after tense negotiations to end postelection violence in which at least 1,000 people were killed in Kenya.
Odinga remains a beloved figure in Kenya, but some saw his recent political alliance with William Ruto, the current president of the country, as a betrayal of a decades-long fight for good governance in the east African country.
As head of the AU Commission, Youssouf inherits challenges ranging from the rise of military juntas in west Africa to a violent rebellion in eastern Congo, where rebels backed by Rwanda have taken two major cities in recent days.
Youssouf has been Djibouti’s foreign affairs minister since 2005.
The AU is frequently criticized for perceived inaction or lack of serious response to armed conflicts in different parts of Africa.
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Rodney Muhumuza reported from Kampala, Uganda.