The CAF executive committee took the unprecedented decision to cede control and have FIFA general secretary Fatma Samoura parachuted in as "FIFA General Delegate for Africa".
A joint statement was read out at a news conference held by beleaguered CAF president Ahmad Ahmad in Cairo on Thursday on the eve of the Africa Cup of Nations but he refused questions on the subject.
Samoura will take over the running of CAF from August to January with the possibility of a renewal of her six-month stint.
Ahmad, who is the subject of an ethics investigation by FIFA after allegations of corruption and sexual misconduct, proposed the idea to colleagues on the executive committee at their meeting in Cairo on Wednesday. It was approved without dissent.
The idea of sending Samoura to Africa is said to have been put together by FIFA president Gianni Infantino and CAF vice president Amaju Pinnick in the wake of Ahmad's brief detention by French police last week for questioning on corruption allegations.
Ahmad, who is seeking to hold onto some semblance of power or even walk away from his post without sanction, had been forced to accept the deal and then propose it to his own colleagues, CAF sources told Reuters.
The statement said Samoura would be assisted by experts in a bid to oversee management of CAF, including governance and administrative procedures.
She would attempt to improve the professionalism of the organisation and support growth and development in all African countries.
FIFA are to also undertake a forensic audit of CAF, it added.
The controversy surrounding Ahmad, who was elected CAF president two years ago, has come as major embarrassment to Infantino, who has been claiming a new-look, clean and corruption-free FIFA.
Ahmad, by virtue of his position as leader of African football, is automatically a FIFA vice president.
African football has been rocked not only by the firing of CAF general secretary Amr Fahmy for whistle blowing, but also a walk off in the Champions League final and the alleged assault on a referee by another of CAF's vice presidents.
The Cup of Nations kicks off in Cairo on Friday when hosts Egypt take on Zimbabwe.
(Reporting by Mark Gleeson; Editing by Christian Radnedge)
