The result also doubles as a historic qualification to the 2027 Women's World Cup for WAFCON debutants Malawi.
Ghana and Malawi had previously faced off in a pre-tournament friendly just weeks prior with the Black Queens easily winning 4-0.
However, it was always going to be a different encouter this time especially after the Scorchers topped Group C with Nigeria, Zambia, and Egypt.
It was a dream start for Kim Lars Bjorkegren's women after Chantelle Boye Hlorkah volleyed home just 7 minutes into the game to give Ghana the lead after seven minutes.
However, Malawi responded just five minutes ater Tenwa Chawinga's effort deflected into the net to draw parity.
Both teams struggled to create anything meaningful till half time. Ghana started the second half with real intent and hought they had taken the lead after Doris Boaduwaa headed an Alice Kusi cross into an empty net.
Unfortunately for the 2024 bronze medallists, VAR ruled the goal out for offside. The game was evenly balanced until Malawi seized the momentum started creating the better opportunities with 20 minutes to go.
Just when it looked like we would see the first extra time at the WAFCON, Rose Kadzere picked up the ball in the box and slotted it below an onrushing Cythia Konlan to give Malawi the lead with just over 10 minutes to go.
The debutants held on and qualified for the semi-finals and in the process made history by qualifyinfg for the 2027 Women's World Cup.
Malawi will next face Algeria in the semi-finals in the WAFCON for a place in the final.
For Ghana, the defeat was a bitter blow to their hopes of returning to the global finals for the first time since 2007.
However, the Black Queens remain in contention for a World Cup place and will now face Cote d'Ivoire in the African play-off, with the winner advancing to the FIFA Women's World Cup intercontinental play-offs.