A field of more than 30 are vying for the presidency in an election already delayed three times this year. None is expected to top the 50 percent of the vote necessary to avoid a runoff, which will take place December 20 between the two candidates with the most votes.
Ousted leader Marc Ravalomanana and current President Andry Rajoelina, who swept into power backed by military coup, were both barred from running.
Instead, Rajoelina has thrown his support behind former Finance Minister Hery Martial Rakotoarimanana Rajaonarimampianina, while Ravalomanana is supporting Avana Party candidate Richard Jean-Louis Robinson.
Rajoelina told reporters after the vote that the election would mean the end of the constitutional crisis, which he brought on by failing to follow through on a promise to hold elections within two years of deposing Ravalomanana.
"The crisis has lasted too long," he said. "We feel the need of the Malagasy to fulfill their duty. The results come from the choice of the people; we must accept it."
Turnout among the island nation's nearly 7.7 million voters is expected to be high, and reports indicated that the day had been largely peaceful.