Stephen Amankonaa struck home for the home side in the 38th minute to lead 1-0 at the half time.
WAFA returned from recess looking to avoid a third consecutive defeat but Berekum Chelsea backline proved difficult to unlock.
The visitors in a tactical switch brought on Jalilu Haruna Mola and Prosper Ahiabu for Richard Danso and Kelvin Boakye Yiadom.
The clock kept ticking down for WAFA but Abubakari Ibrahim was on hand to equalize for his side in a goal-mouth melee in the 72nd minute.
With the game appearing to end in a draw, WAFA scored the match-winner four minutes into added time.
Eric Asamany was the goalscorer this time as WAFA took all three points at the Golden City Park.
The win will come as a relief for the Academy boys who will play Bechem United next while Berekum Chelsea face Medeama SC.