WAFA striker Daniel Lometey scored all two goals in Maradi coupled with some good goalkeeping from Belgium-based Manaf Nurudeen.
The Black Satellites profited from some sloppy defending by the young Stallions to score the pair of goals in Maradi.
Lomotey won the physical battle against centre back Kone inside the box and lobbed the ball over goalkeeper Traore for the opening goal just on the nick of half time.
In the 77th minute, the burly striker used his strength to bully Kone inside the Burkina Faso area to lift it above and over the goalkeeper.
Ghana will play joint leaders Senegal on Wednesday and will book an early 2019 FIFA U20 World Cup qualification ticket if they win.