Forward Justus Torsutsey scored a late penalty as WAFA secured their first victory in the Ghana Premier League this season.
Coming into the game, the Academy Boys had drawn two and lost two so they were under pressure but Olympics didn't make it easy for them.
WAFA had to wait until the 90th minute when they awarded a contentious penalty.
Torsutsey beat the goalkeeper and hand WAFA three points, while Olympics lost for the first time this season.
Watch highlights of the match below