Form favours the Malagasy as they edged their Group A opponents 1-0 away two days ago thanks to an early goal from France-based Faneva Andriatsima.
Thailand-based midfielder Njiva Rakotoharimalala scored the only goal of the game right at the end of the first half.
The result puts Madagascar on 10 points in Group A to guarantee them a place in next year’s finals, which are set to be hosted by Cameroon.
It will be the first time that 24 teams will feature in the competition.
Senegal will join them in the finals if they can win in Sudan later on Tuesday.
There are two more qualifying rounds left to play, one in November, and the final matches will be in March next year.