CAF, leading 3-2 from the first leg, claimed a 1-1 draw in Bangui to advance to the final round of qualifiers for the 2013 tournament.
Foxi Kethevoama headed CAF into the lead in the 23rd minute and even though Emad Metab levelled 13 minutes from time, Egypt could not find the two further goals they needed to go through.
CAF are yet to reach the finals of a major continental competition, while Egypt have won the Nations Cup seven times, most recently in 2010.
This is the first time they have failed to qualify for two successive tournaments after they missed out on the 2012 finals earlier this year in Gabon and Equatorial Guinea.
England will debut their new away jersey against Brazil at the Maracana Stadium on Sunday. Get in the Gear
Barcelona will wear this new home soccer jersey next season. They also have a new away jersey. Get them both.
Jamaica is in need of a win against the U.S. Get the jersey of the Reggae Boyz.
Neymar's move from Santos to Barcelona is no doubt the biggest summer transfer.
Germany is one of the top teams ever and they will play the US on Sunday.
The hoop soccer jersey is classic and cool. The USA hooped jersey is perfect for every fan. Get in the Gear.
Support the USA national team with an official 2013 Centennial soccer jersey from Nike. Its Official.
The Nike Hypervenom is the latest cleat silo from Nike. It will change your game and is worn by the game's top players.
The adidas Nitrocharge is the most talked about new cleat in years. It was released on May 15 and will take your pitch by storm.
The USA will wear their blue away jersey against Jamaica in their World Cup qualifier on Friday night.