Kennedy Boateng fired WAFA into the lead, before Kwamla Agbenagah doubled the lead for the academy boys.
Back from recess Wa All Stars snatched the consolation goal through Matthew Andoh.
The defeat has enabled Wa All Stars to surrender their lead at the summit of the league ladder to Hearts of Oak who secured a 1-0 famous victory at Essipong against Hasaacas.