At a packed event in the capital Antananarivo, election authorities assigned the 13 presidential candidates their ranking on the ballot voters will use to choose the next head of state on Nov. 9.
Rajoelina was handed number three but much of the political discourse in the Indian Ocean island focused on a weekend decision by the Constitutional Court to dismiss appeals seeking to void his candidacy.
"Drawing number three is no coincidence. It's the trinity. It's the winning three, it is the Father, the Son and the Holy Spirit," Rajoelina told AFP at the electoral commission headquarters after the draw.
Media reports in June revealed that Rajoelina had been naturalized as French in 2014.
Under local law that meant he could lose Madagascan nationality and thus the ability to lead the country and run for office.
This version of the facts was vigorously disputed by the ruling party.
On Saturday the Constitutional Court rejected appeals filed by three opposition parties to have Rajoelina's name struck off the ballot as "unreceivable."
The 49-year-old subsequently resigned as the constitution requires sitting heads of state to do before contesting a presidential election.
'Worried about democracy'
The Senate president was supposed to take over but declined to do so for "personal reasons," handing the reins to a "collegial government" headed by a close ally of Rajoelina — sparking further controversy.
"We cannot have clear confidence in the neutrality of this collegiate government," said Alain Desire, a representative of the party of former President Hery Rajaonarimampianina.
Presidential candidate Siteny Randrianasoloniaiko told AFP he was "worried about (the state of) democracy" in the country.
Rajoelina had not waited for the court ruling to announce his candidacy, holding a grand campaign launch at a stadium in the capital last week.
He first took power in 2009 on the back of a coup that ousted former president Marc Ravalomanana, who is also running in November.
After not contesting in the 2013 election due to international pressure, Rajoelina was voted back into power in 2018.
Madagascar is one of the poorest countries on the globe despite vast natural resources. Some 80% of the 28 million population live on less than 1.92 dollars per day.
If no candidate wins more than 50% of the votes, a run-off will take place on December 20.
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