Rajoelina is one of 13 candidates on the ballot but 10 of the others have called on voters to shun the elections, complaining of an "institutional coup" in favor of the incumbent.
Following a night-time curfew and weeks of protests, voting got calmly under way early Thursday, with voters emerging from rudimentary polling centers, their thumbs stained with green and gold indelible ink.
Polls are scheduled to stay open until 05:00 pm (1400 GMT).
The incumbent president has brushed off criticism and expressed confidence that he will secure re-election in the first round of voting.
After casting his ballot in the capital, Antananarivo, Thursday, Rajoelina urged voters to do the same.
"The only democratic path... are elections," he said, denouncing people "who try to cause trouble."
Eugene Rakatomalala, a 43-year-old voter said, "I'm voting, but we know this isn't normal."
"There weren't any candidates who did campaigns," the voter added.
Roland Ratsiraka, one of the protesting candidates, on Tuesday said, "we do not want to participate in this fraud, it is a joke on Madagascar."
Since early October, the opposition leaders have led near-daily, largely unauthorized protest marches in the capital. They have been regularly dispersed by police firing tear gas.
While the opposition refused to campaign, Rajoelina flew across the country by private plane, showcasing schools, roads and hospitals built during his tenure.
Lalatiana Rakotondrazafy, Rajoelina's campaign spokesperson said, "it is irresponsible to encourage voters not to vote."
Alain Randriamandimby, a T-shirt printer in Madagascar said "we don't want any more demonstrations, we don't want any more problems in the country. We want to choose for ourselves, by voting."
At a news stand on Wednesday, residents looked concerned as they scanned newspaper headlines.
Chrishani Andrianono, a 55-year-old Madagascan said, "people have become aware of the dictatorship we live under," complaining that after 11 years in power, the incumbent president had little to show for it.
"We do not see what he did for us," Andrianono added.
Josiane Rasomalala, a 41-year-old from Madagascar supported Andrianono's sentiments.
"In the morning, I don't eat — only a little at lunchtime and in the evening. Otherwise, I can't get by, I don't have enough," Rasomalala, said, adding, "I'm voting because we need a better life."
Authorities in Madagascar imposed a night-time curfew on Wednesday in Antananarivo, following what police said were "various acts of sabotage."
The local police prefect later said an investigation had been opened after electoral material stored at three polling stations was burned on Tuesday.
Madagascar has been in turmoil since media reports in June revealed Rajoelina had acquired French nationality in 2014.
Under local law, the president should have lost his Madagascan nationality, and with it, the ability to lead the country, his opponents said.
Rajoelina has denied trying to conceal his naturalization, saying he became French to allow his children to pursue their studies abroad.
His challengers were further enraged by another ruling allowing for an ally of the president to take over the reins of the nation on an interim basis after Rajoelina resigned in line with the constitution to run for re-election.
They have also complained about electoral irregularities.
The head of the electoral commission, who critics accuse of favoring the president, on Thursday said some voters did not receive their electoral cards on time.
This was "either because we did not have the correct address, or because they were not at home during the distribution," said Arsene Andrianarisedo.
The opposition grouping has vowed to continue protesting until a fair election is held.
Eleven million people registered to vote in Madagascar's 2023 elections.
The Southern African Development Community, SADC, a regional bloc, as well as the African Union and the European Union, have sent observer missions to monitor the vote.