The Doboro-based side triumphed 6-5 during the spot kicks to seal the win in their round of 32 contest.
After a regulation time, both teams were level at 1-1.
But it was Wise who converted all their penalties and won it in sudden death.
WAFA coach Prosper Narteh Ogum paid for his decision to rejig his team sheet by fielding fringe players.
Young Wise are through to the round of 16.
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