The election, held in Addis Ababa, Ethiopa, saw Ahmad prevail by 34 votes to 20.
The result ends the 29-year reign of Hayatou as Africa's football ruler.
"Ahmad's victory is testament to his determination to positively alter the 29-year status quo in CAF", Saraki said in a statement by his Special Adviser on Media and Publicity, Mr Yusuph Olaniyonu.
Mwendwa, alongside 53 other Africa based Football Association's presidents, will on Thursday vote for the next president of the continental football body.
The 12-member Council of East and Central Africa Football Associations (CECAFA) adopted a resolution in February to back Hayatou, but an Egyptian official told AFP that "a small coalition" including Morocco, South Africa, Zimbabwe and Egypt will support Ahmad. He will become a Federation Internationale de Football Association vice president and join the council.
Ahmed has said that his first task will be to introduce a new code of ethics that will effectively check stakeholders in football on the continent.More news: Ronald Koeman makes worrying admission about Ross Barkley's future
Hayatou headed CAF since 1988 and is a senior vice president of Federation Internationale de Football Association.
Speaking before the election, outgoing CAF boss, Hayatou lauded the Ethiopian authorities, the African Union and the Ethiopian Football Federation for the support and efforts made towards the success of the event.
Hayatou was finally beaten by a man who promised to modernize CAF and make it more transparent. Jordaan had been one of Ahmad's primary backers as SA joined the rebels in the build-up to Thursday's vote. Neither did he respond to this newspaper's texts.
The 70-year-old from Cameroon left the congress room briefly without commenting when the result was announced, led away by the arm by one of his aides.
Then the man who ruled African football for almost 30 years, Hayatou, had to be dragged out of the Nelson Mandela Hall, ignoring journalists requests for comment.