Karela United relegated WAFA from the Ghana Premier League posted a 1-0 victory over the academy side on Sunday.
Midfielder Umar Bashir scored the only in the second half to send his former club to the second-tier.
The Passioners were determined to end the season with a win and tighten their grip on the fourth spot.
WAFA went into the match needing three points to survive eviction on the final day of competition.
But they lacked the fortitude to go past their hosts and could barely threaten them.
WAFA finished second-bottom the table.