As recently as August, Assimi Goita was involved in another military coup when then-President Ibrahim Boubacar Keita was ousted.
Goita was then appointed interim president.
On Monday, it was Goita who ordered the arrest of President Bah N'Daw and Prime Minister Moctar Ouane.
They resigned on Wednesday while still in custody and were released on Thursday.
Concerns about al-Qaeda and IS
The 15 West African countries that make up the Ecowas economic community, together with France and the United States, have expressed concern about how the takeover will affect the situation in northern and central Mali.
The areas are a central base for local supporters of the terrorist organizations al-Qaeda and IS.
The situation in Mali was raised during the EU leaders' summit in Brussels this week.
Together with the UN, the United Kingdom, the United States, the African Union and Ecowas, the coup attempt was condemned in a joint statement.
EU Council President Charles Michel said the EU was "ready to take the necessary action".
Coup makers want to appoint new prime minister
On Sunday, Ecowas heads of state will meet in Ghana.
The leaders want Mali to be led civilly until the elections in February.
During the military coup in August, the organization said that Vice President Goita "under no circumstances can replace the president" during the transition phase until the election.
On Friday, Assimi Goita announced on national television that he will appoint a new prime minister from among the members of the M5-RFP coalition.
It is the organization that led the protests against Keita in August.