The electoral commission said on Friday that Rajaonarimampianina, the candidate backed by outgoing President Andry Rajoelina who spearheaded the coup nearly five years ago, won 53.5 per cent of the December 20 vote.
He beat Jean Louis Robinson, who ended up with 46.5 per cent and has demanded a recount.
Robinson’s camp has filed almost 300 complaints to the electoral court, which has to rule on the commission’s provisional result by January 19.
Celebrations were muted in the capital, Antananarivo, where Rajaonarimampianina had struggled to win support in the first round.
“I urge the Malagasy people to await the final result in complete serenity,” Rajaonarimampianina told reporters.
Asked about the vote fraud allegations, he said: “It’s (Robinson) who says that and not the people.”
Robinson stayed away from the results declaration.
“We have said all along there was massive electoral fraud across Madagascar,” said Elyse Razaka who helped run Robinson’s campaign.
“Robinson won’t order people to take to the streets. But it is different if there is a spontaneous movement.”
The poll is meant to end a crisis that has driven out investors, cut aid flows and sharply slowed the economy.