Ghana eliminated Benin in the preliminary round to set up a Jollof derby against bitter rivals Nigeria in the final round of qualifiers.
Super Eagles were hoping to make it to the tournament next year after missing out on the last edition.
The Salisu Yusuf managed team did well to hold their own in the first half which ended 0-0.
Black Galaxies of Ghana went in front through Daniel Afriyie Barnie who scored a spot kick in the 48th minute.
Four minutes from time, Seidu Suraj gave Ghana a good advantage with the second goal of the game.
The return leg is scheduled for Saturday, 3rd September at the MKO Abiola National Stadium, Abuja.
Super Eagles XI: Adeyinka Adewale, Tope Olusesi, Ebube Duru, Samson Gbadebo, Afeez Nosir, Joseph Onoja, Bello Babatunde, Chijioke Akuneto, Andy Okpe, Abubakar Sadiq