Madagascar’s winning goal came after 42 minutes by Njiva Rakotoharimalala and the Malagasy team became the first to qualify for the tournament.
Following the victory, Madagascar reached 10 points to lead the group with two matches to spare; they are three points ahead of Senegal who will face Sudan at the other group game.
Madagascar played in Group A alongside Equatorial Guinea, Senegal and 1970 African Cup of Nations champions, Sudan.
They started their journey with an away 3-1 victory over Sudan and then they secured a 2-2 draw at home against their toughest opponent in the group, Senegal.
The islanders, led by French manager Nicolas Dupuis, achieved back to back victories over Equatorial Guinea to win their first qualification.
Madagascar squad includes Misr Lel Makasa striker, Paulin Voavy, who has been a key player to the team during the qualifiers.