The country's highest court was now expected to formalise the appointment of Colonel Michael Randrianirina in a ceremony at 10:00 am (0700 GMT), capping a dramatic week in which Rajoelina was impeached for desertion of duty on Tuesday, with the military stepping in.
Amid international criticism, including from the United Nations, Randrianirina denied he had initiated a coup, pointing to the constitutional court's backing of his new role.
A large crowd gathered for the ceremony at the court Friday with representatives of a youth-led movement, which spearheaded protests that led to Rajoelina's fall, rubbing shoulders with politicians.
Foreign delegations, including from the United States, the European Union and the French ambassador, were also present, an AFP journalist said.
The 51-year-old commander of the CAPSAT unit has pledged elections in 18 to 24 months and told local media that consultations were under way to appoint a consensus prime minister.
"Madagascar has not chosen a military regime," he told reporters Thursday.
"The government belongs to civilians. The presidential council is also composed of military and civilians," he said.
Rajoelina's camp has condemned the constitutional court's support of the CAPSAT commander as riddled with procedural illegalities that risked destabilising the former French colony.
It has insisted that Rajoelina remain leader and was working to find solutions to the problems dogging the impoverished island, including power cuts that sparked a youth-led protest movement on September 25.
Government forces were accused of a harsh crackdown on the protesters, with many reported dead or wounded, until CAPSAT announced on October 11 that it would refuse orders to shoot on them.
The statement was a turning point in the uprising, with the unit hailed by the protest movement, which is now expecting a role in the new set-up.
- Escape, hiding -
Rajoelina's office confirmed in a statement late Wednesday that he fled the country the same weekend CAPSAT stood behind the protesters, saying he feared for his life. He did not reveal his whereabouts.
Media reports said the 51-year-old was evacuated on Sunday aboard a French military plane that took him to the French island of Reunion from where he travelled to Dubai.
Madagascar is the latest of several former French colonies to have fallen under military control since 2020, after coups in Mali, Burkina Faso, Niger, Gabon and Guinea.
It is the third military transition in Madagascar since independence from France in 1960, following coups in 1972 and in 2009.
The country, off Mozambique, is one of the poorest in the world, despite an abundance of natural resources and a rich biodiversity.
About 80 percent of its roughly 32 million people live in poverty, according to the World Bank's benchmark.
Rajoelina's escape is the third time a Malagasy head of state has left the country after being ousted. Didier Ratsiraka fled to France in 2002 after post-electoral violence and Marc Ravalomanana went to South Africa in 2009.
The African Union and regional SADC bloc said they would send fact-finding missions to the island and called for constitutional democracy to be upheld.
"The transition is now underway. We call for the full involvement of civilians in the ongoing process," French Foreign Minister Jean-Noel Barrot said Thursday.
"The mobilisation of Madagascar's youth must be fully heard to build a sustainable, peaceful, and calm solution," he told reporters during a visit to Nigeria.
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