The goals were scored by Jordan Ayew and Thomas Partey in the 46th and 72nd minutes of the game.
Ghana drew 2-2 with Benin in the first match and played a goalless against the Indomitable Lions of Cameroon in the second match.
It was a goalless first half in the two Group F games in Egypt as Guinea-Bissau held Ghana whiles Benin also continued to defy holders Cameroon.
A minute after half time, Ghana took the lead against Guinea Bissau, a fellow West African country.
Midfielder Thomas Partey sealed Ghana’s qualification to the next round in the 72nd minute.
Mubarak Wakaso was adjudged the man of the match.
-Graphic