Bruno Nongoma Zidouemba, the chairman of the AU's peace and security council, said that "what occurred in Madagascar enters the definition of unconstitutional change of government".
"The council then decided to suspend the participation of Madagascar to the bodies and organs of the AU," he said.
Despite the criticism, Madagascar's courts and army have backed Rajoelina, who forced Ravalomanana from the presidency on Tuesday after a seven-week campaign of street protests.
On his first day in office, the 34-year-old Rajoelina dissolved the senate and national assembly without opposition.
After losing control of the government and the army, Ravalomanana, 59, gave up power to a military directorate, which in turn passed it to Rajoelina.
Madagascar's constitutional court on Wednesday ruled that the double-transfer was legal and that Rajoelina was the country's rightful interim leader.
The interim leader has promised to bring food prices down on the island, where three-quarters of the population live on less than $2 a day.
He also said he would sell a plane that Ravalomanana recently bought for $60m, and use the money "to establish a hospital for the people's health, which is a higher priority".
Rajoelina has also cancelled an agreement to lease South Korean corporation Daewoo more than a million hectares of land to grow food crops, a deal for which Ravalomanana was heavily criticised.
The United States said on Friday that it would halt all non-humanitarian aid to the Indian Ocean island.
"This series of events is tantamount to a coup d'etat," Robert Wood, the US state department spokesman, said. "In view of these developments, the United States is moving to suspend all non-humanitarian assistance to Madagascar."
Wood said he was not able to say precisely how much aid would be affected.
Ravalomanana's whereabouts are still unknown following his removal from power.
The new leader has said Ravalomanana should be prosecuted for alleged crimes, including the use of lethal force against unarmed opposition demonstrators in recent weeks.
His government has banned Ravalomanana's ministers from leaving the country.