The southern Africans scored three goals in the first half of the game on Monday night and held on to complete the game without conceding a goal.
Olivier Tokinantenaina opened the scoring just 13 minutes into the fixture before Solom Raza and Lalaina Rafanomezantsoa got onto the scoresheet to extend the lead for Madagascar.
The win sees Madagascar take nine points from three games having been awarded three points for Morocco’s no-show at the tournament while also beating Ghana in their group opener.
The result also means the Black Galaxies comes second in their group, three points shy of Madagascar and three points clear of Sudan, who exit the competition after finishing third in the group.
Ghana and Madagascar will have their fate in the competition determined in the upcoming games in Groups D and E respectfully.