The Ghanaian champions claimed all three points at the Suez Canal Stadium in Ismailia, Egypt, thanks to a late strike from Beline Nyarkoh.
Ampem Darkoa started brightly and took the lead in the eighth minute when Nancy Amoh capitalised on a goalkeeping error to put her side ahead.
Kawempe Muslim responded positively and restored parity in the 33rd minute through Shadia Nabirye, ensuring the teams went into half-time level at 1-1.
The Ugandan side continued to compete after the break, making life difficult for their opponents as both teams searched for a decisive goal.
However, Ampem Darkoa found the breakthrough in the 83rd minute when Nyarkoh scored to put the Ghanaian champions back in front.
The late goal proved decisive as Ampem Darkoa held on to secure a 2-1 victory and collect their second successive win in the competition.
Ampem Darkoa move top of Group B
The victory takes Ampem Darkoa to six points from two matches following their impressive 5-1 opening victory over Mali's USFAS Bamako.
Their latest result strengthens their position at the top of Group B and puts them in a strong position to qualify for the semi-finals.
Kawempe Muslim, meanwhile, will look to recover from the defeat after making an impressive start to their tournament with a 3-2 victory over defending champions AS FAR Rabat.
Ampem Darkoa will face AS FAR in their final group-stage fixture as they seek to secure qualification for the knockout rounds.
Full-time: Ampem Darkoa Ladies 2-1 Kawempe Muslim Ladies
Goalscorers:
• Ampem Darkoa Ladies: Nancy Amoh 8', Beline Nyarkoh 83'
• Kawempe Muslim Ladies: Shadia Nabirye 33'