In the second half, the Moroccan team returned to dominate play and score a brace through Soufiane Rahimi, Hamza El Moussaaoul and an own goal by goalkeeper Charles Lukwago.
Saidi Kyeyune netted a consolation goal for Uganda Cranes. The defeat means Uganda exited the sixth edition of the Chan tournament bottom of Group C with one point after their 0-0 against Rwanda.
Coach Jonathan McKinstry’s team also lost 2-1 to Togo. In another Group C match played at the Limbe Omnisport stadium Rwanda came from a goal down to defeat Togo 3-2 to qualify for the quarter-final stage.
Olivier Niyonzima, Jacques Tuyisenge and substitute Ernest Sugira scored for Rwanda, Yendoutie Nane and Bilal Akoro netted for Togo.
Rwanda now joins Morocco, Mali, Congo Brazzaville, DR Congo and hosts Cameroon in the quarter-finals. The last games in Group D will be played on Wednesday with Namibia facing Zambia, while Tanzania takes on Guinea.