The Red Star Belgrade goal poacher, who received a late call-up to replace Raphael Dwamena, scored the first and last goals at the Stade de Kintele in Brazzaville.
In the 85th minute he controlled a pass from Harrison Afful inside and coolly placed it at the blind side of the Congo goalkeeper.
In between that, his shot at goal fell to Thomas Partey to slot in the goal.
Boakye was the highest scorer with seven goals in the qualifying rounds of this season's UEFA Europa League where his side advanced to the Group stage.
He last played for Ghana at the 2013 African Cup in South Africa.
From Sammy Heywood Okine