Hayatou, 64, fainted during a closed session late on Thursday and was taken to hospital in the Egyptian capital for tests. He was kept in overnight for observation.
CAF media director Suleiman Habuba tells The Associated Press on Friday "the condition of Hayatou is stable. He has suffered from stress in the past but now he is in good health."
Habuba says Hayatou could still attend the conference's closing ceremony later on Friday.
Hayatou, of Cameroon, has been CAF president for 23 years. He is a FIFA vice president and member of the World Cup organising committee.