The Black Queens failed to get past the first round of the African Women Championship despite a win in their final Group B game.
Ghana came from a goal down to beat Tunisia 3-2 but it was too little too late Nigeria joined South Africa in qualifying for the semi-finals after the defending champions had claimed a 1-0 victory over the Bayana Bayana.
The Black Queens, pre-tournament favourites picked the ball from the post just after four minutes of play when the Tunisians scored the opener. Ghana drew level on the stroke halftime.
But back from recess and the Tunisians jumped into the lead again, scoring the second goal three minutes into the half.
In the 51dt minute, Safia Abdul Rahman restored parity on the scorecards, giving Ghana the equaliser before going on to seal the winner in the 82nd minute.
The tournament, hosted by Equatorial Guinea enters the semi-final stage on Tuesday.