The decision means that Rajoelina, who was to be brought before the court since he left the country after several weeks of protests, will not be able to stand in future elections.
According to a decree, Rajoelina's citizenship was withdrawn because he had obtained French citizenship in 2014, reports local media.
The leader of the military coup, Colonel Michael Randrianirina, has previously been sworn in as the country's new president.
The events have unfolded after weeks of youth-led protests against corruption, unemployment and recurring power and water shortages that developed into increasingly loud demands for the president's resignation.
