The Ghanaian champions were beaten 4-1 on penalties after the final ended 2-2 after 90 minutes at the August 4 Stadium in Ouagadougou, Burkina Faso, on Saturday.
Ampem Darkoa made a perfect start to the contest when Beline Nyarko put them ahead just two minutes into the game.
Edo Queens responded almost immediately, with Doosuur Anastasia Atume restoring parity two minutes later.
The two sides remained level for much of the match before Nyarko struck again in the 74th minute to put Ampem Darkoa back in front.
The Ghanaian champions looked set to hold on for the regional title, but Edo Queens produced a late comeback when Oluebube Umejiaku scored in the fourth minute of stoppage time to make it 2-2 and force the match into a penalty shootout.
Edo Queens proved more composed from the spot, converting all four of their penalties, while Ampem Darkoa scored only one of their attempts to lose the shootout 4-1.
The victory secured Edo Queens the sole WAFU Zone B ticket to the 2026 CAF Women’s Champions League.
The defeat is a disappointing end to what had otherwise been an impressive campaign for Ampem Darkoa.
The Ghanaian champions had won all four of their matches before the final, including a 2-1 victory over Edo Queens in the group stage. They went on to beat Benin's FC Dynamique 4-1 in the semi-final, with Milot Pokuaa scoring twice.
Edo Queens, meanwhile, reached the final after defeating hosts USFA 5-1 in their semi-final.
Despite losing to Ampem Darkoa in the group stage, the Nigerian champions recovered when it mattered most to claim the WAFU B title and book their place in the continental competition.
For Ampem Darkoa, the result means their hopes of returning to the CAF Women’s Champions League have ended, with Ghana once again missing out on representation in the competition.
