The Pharaohs have been occupying the ninth spot for the past three months but could not hold onto it after their lackluster performance cost them what was expected to be an easy victory over tiny Niger. They now lie 11th.
Niger's stunning victory over Egypt saw them move to the 100th spot after climbing 54 places.
Croatia and Russia climbed into the top ten after registering victories in EURO 2012 qualifiers.
Egypt remained on top of the African teams though, six places above World Cup quarter-finalists Ghana, who are ranked 17th.
The seven-time Nations Cup winners next face Australia in a friendly game on November 17th.
World champions Spain and runners-up Holland remained first and second respectively in the ranking table.
Top five African teams:
11-Egypt
17-Ghana
19-Ivory Coast
33-Algeria
34-Nigeria