Taher Mohamed Taher's header and a late goal from Hossam Hassan were not enough as Smouha secured a vital win over Al Ahly.
After announcing a 25-player list for the competition on Wednesday, Carlos Queiroz changed his mind and decided to add three players to the list.
Egypt had several clear chances to have the lead but all the efforts of Mostafa Fathy, Marwan Hamdy and Mohamed Sherif did not find the target.
Egypt tops Group F with 10 points after four matches as they only dropped two points at a draw against Gabon away from home.
Queiroz included Afsha and Sherif in his list after ruling them out of the two matches against Libya last October.