The Black Satellites came into the game on the back of a 4-0 thumping of Tanzania and a goalless draw against Morocco.
However, Karim Zito’s side failed to replicate their form against the Gambians. Having taken an early lead through Abdul Fatawu Issahaku, Ghana laboured to keep their opponents at bay.
Kajally Drammeh draw the Gambians level in the 16th minute, before Lamarana Jallow scored what proved to be the winner before half-time.
The result sees Ghana finish in third place in Group, with Morocco and Gambia finishing first and second, respectively.
Meanwhile, the Black Satellites will now face Group A winners and tournament favourites Cameroon after finishing as one of the third best-placed teams.
Cameroon, though, won all three of their games in Group game, scoring six goals and conceding just once.