The Moroccans clinched their place thanks to three second-half goals from JawadYamiq, AbderrahimMaqran and Badr Belhrouz.
Hamid Hossam scored a late consolation goal for Egypt, who were making their debut in the biennial competition for home-based footballers.
Algeria knew they had to score at least twice against Libya to survive having lost the first leg 2-1, and they took the lead midway through the first half when SofianeBendebka scored off a rebound.
But first-leg match-winner MuaidEllafilevelled on the stroke of half-time and Libya held on to take the aggregate win.
Despite CHAN matches only featuring locally based footballers the games have full international status and count toward the monthly FIFA rankings.
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