كتب : Omar AbdelAziz
The Algerians went into the game knowing that a draw is enough to keep them on top of Group 8, but they were stunned by goals from French-based duo Node Mansare and Pascal Feindouno.
Leaders Guinea are level with Algeria on 8 points, but the latter trail by a 2-goal difference.
The win inched Guinea closer to qualifying as they have a remaining home game against minnows Cape Verde while Algeria will visit Gambia.
Gambia and Cape Verde shared the points in a goalless stalemate, and they both have no chances of making the finals, tying at 5 points.
Elsewhere, Algeria's North African Neighbors Tunisia have booked their place in the Ghana finals with an easy 2-0 win against Mauritius.
Issam Jomaa scored the first goal one minute before the break and Sfaxien playmaker Abdul-Karim Nafti added the second on the hour mark.
The Tunisians are in charge of Group 4 with 13 points, one point ahead of Sudan as the Arab duo secured a place in the finals.