The self-made millionaire, driven from power by disc jockey-turned-politician Andry Rajoelina, boarded a commercial South African flight in Johannesburg on Saturday morning, saying he was confident of a safe return, despite threats that he would be arrested on arrival.
But in mid-flight, Madagascar closed its airspace, forcing the aircraft to head back to Johannesburg.
Ravalomanana's spokesman Peter Mann warned the refusal to allow the plane to land would have dire consequences for an agreement signed last year by the island's main parties in a bid to steer the country toward elections.
Thousands of people had filled the road leading to Antananarivo's airport from the capital, blocking all traffic as they sought to greet Ravalomanana.
A transitional government was formed in November, in a deal that allows the return of political exiles. Another deposed leader, Didier Ratsiraka, recently returned from exile in France without incident.
But security forces had warned Friday that Ravalomanana would be arrested if he returned, after he was sentenced to life in prison and hard labour for the death of 30 opposition protesters killed by his presidential guard in February 2009.
Roland Ravatomanga, an aide to Ravalomanana who was named agriculture minister in the unity government, said the decision to shut down the nation's airspace was a "surprise".
"It's clear that the transitional president (Rajoelina) doesn't want to apply the roadmap. For us, it's a unilateral decision, as usual," he told the French news agency.
Madagascar has been isolated by the international community since Ravalomanana's ouster, with the African Union and the Southern African Development Community suspending its membership until a return to constitutional order