The High Constitutional Court has nine days from Thursday to decide whether to confirm the provisional results.
Rajoelina’s rival Marc Ravalomanana on Sunday alleged fraud.
Rajoelina won 55.66 % of the vote compared to 44.34 % for Ravalomanana, and turnout was just over 48%, the commission said.
The two ex-presidents, Ravalomanana and the man who ousted him in a 2009 coup, Rajoelina, had previously said they would accept the results, raising hopes of a peaceful outcome and no repeat of the political chaos seen nearly a decade ago.
Rajoelina attended the commission’s results announcement on Thursday. Ravalomanana did not.
The Indian Ocean island nation has a population of around 25 million people and is among Africa’s poorest. About 80% of the population lives on less than $2 per day.