Ahmad Ahmad of Madagascar and Issa Hayatou, who is from Cameroon.
The 57-year-old former government minister, who goes by just a single name, won the CAF presidency by 34 votes to 20 in the poll, bringing to a surprise end the 29-year tenure of the 70-year-old Hayatou, who is from Cameroon.
The result was greeted by cheers at the CAF Congress as Ahmad was carried on the shoulders of jubilant supporters to the podium after the result was announced.
Ahmad, previously minister of sport and minister of fisheries in his home country, had been given little chance just a month ago when he announced his candidacy. But he offered voters a fresh face to a younger generation of football association presidents that have emerged.
Hayatou’s long career in football is now at an end, although he is still an International Olympic Committee member.
"It is not that bad," Hayatou, who was first elected in 1988, told reporters as he departed the hall.