Motsepe, 59, from South Africa, was elected unopposed at the organisation’s congress in the Moroccan city of Rabat.
The billionaire mining magnate succeeds Ahmad Ahmad who was elected four years ago but suspended last November on corruption charges.
He is the eighth president in the 64-year history of the continent's governing body.
His ascent was sealed in a deal last week in which the three other candidates Augustin Senghor, Jacques Anouma and Ahmed Yahya, agreed to withdraw from the presidential race in return for top roles in Caf.
Motsepe, who is the brother-law of the South African president Cyril Ramaphosa, began his rise to riches in the late 1990s as a specialist in mining rights.
After acquiring several gold mines, he went on to invest in the extraction of platinum, copper and iron.
Motsepe, the owner of the Mamelodi Sundowns football team, says he wants the Africa Cup of Nations - Caf's most prestigious national team tournament - to remain a biennial event rather than once every four years like its European counterpart and the World Cup.
