The Ghanaian champions needed at least a draw at the Suez Canal Stadium in Ismailia, Egypt, to secure qualification for the semi-finals but were unable to overcome the Moroccan side.
After a closely contested first half, AS FAR eventually broke the deadlock in the 59th minute through captain Ghizlane Chebbak, who found the net to put the defending champions in front.
Ampem Darkoa pushed for an equaliser as they sought to keep their qualification hopes alive, but AS FAR remained disciplined defensively and limited the Ghanaian side's opportunities.
The Moroccan champions then sealed the victory in stoppage time when Youssoufi scored in the 90th+6 minute to make it 2-0 and confirm their place in the last four.
The defeat ended what had been an encouraging campaign for Ampem Darkoa, who entered the final group game with two wins from their opening fixtures.
They began with an emphatic 5-1 victory over Mali's USFAS Bamako before coming from behind to beat Uganda's Kawempe Muslim Ladies 2-1, with Beline Nyarkoh scoring a late winner.
However, the loss to AS FAR left Ampem Darkoa third in Group B with six points, level with both AS FAR and Kawempe Muslim Ladies.
AS FAR topped the group with a superior goal difference, while Kawempe secured the second qualification spot after defeating USFAS Bamako 3-0 in their final fixture.
Agnes Nabukenya scored twice for the Ugandan side, with Jovia Nakagolo also finding the net to secure their historic passage into the semi-finals.
Ampem Darkoa's elimination brings an end to their hopes of improving on their fourth-place finish at the 2023 edition of the competition, having returned to the continental stage after a dramatic qualification campaign.
