Ghana took the lead with eight minutes left to play as Dennis Korsah sent an incisive ball to Umar Basiru, who dribbled past two Benin defenders before cutting a lovely ball across the face of goal to set up Afriyie Barnieh who smashed home.
Ghana will now face sworn rivals Nigeria in the final round in search of a ticket to the CHAN to be held in Algeria.
The Black Galaxies have yet to appear in the tournament since 2014 when Ghana finished 2nd in South Africa.