Keita, embattled by months of protests over economic stagnation, corruption and a brutal Islamist insurgency, said he had resigned to avoid bloodshed.
There were few obvious traces of the previous day's drama in the capital Bamako -- there were no troops on the streets despite the coup leaders announcing a night-time curfew.
The burnt-out home of the former justice minister after an attack by protesters was one of the few visible signs of the overthrow.
A building owned by the Malian Minister of Justice Kassim Tapo, that has been burned and looted in Bamako, Mali, on August 19, 2020, the morning after rebel troops seized Malian President Ibrahim Boubacar Keita and Prime Minister Boubou Cisse in a dramatic escalation of a months-long crisis. Annie Risemberg | AFP
Jubilant crowds had cheered the rebels on Tuesday as they arrived in Bamako, where they detained Keita along with Prime Minister Boubou Cisse.
UN Secretary General Antonio Guterres demanded the "immediate and unconditional release" of both men as diplomats in New York said the Security Council would hold emergency talks on Wednesday.
It was unclear whether Keita was still in custody on Wednesday at the Kati military base -- a facility seized by the mutineers that was also the site of the 2012 coup that brought him to power.
The coup leaders appeared on television overnight to pledge a political transition and new elections within a "reasonable time".
Mali President announces resignation on state television
Malian Air Force deputy chief of staff Ismael Wague said he and his fellow officers had "decided to take responsibility in front of the people and of history".
There were no reports of casualties during the military takeover but the coup leaders announced a curfew and border closures, in effect sealing off the country.
Debris is seen next to a building that has been burned and looted in Bamako, Mali, on August 19, 2020, the morning after rebel troops seized Malian President Ibrahim Boubacar Keita and Prime Minister Boubou Cisse in a dramatic escalation of a months-long crisis. Annie Risemberg | AFP
French President Emmanuel Macron was among the first to condemn the mutiny, his office saying that he still supported mediation efforts by other West African states.
Mali is the cornerstone of French-led efforts to roll back jihadists in the Sahel, and its neighbours are anxious to avoid the country sliding into chaos.
Colonel Wague said "all past agreements" would be respected, including Mali's support for anti-jihadist missions in the region.
"MINUSMA (the UN force in Mali), (France's) Barkhane force, the G5 Sahel, Takuba (a European special-forces initiative) remain our partners," he said.
The coup leaders also remain "committed to the Algiers process," a 2015 peace agreement between the Malian government and armed groups in the north of the country, he said.
Years of fighting have failed to brake an Islamist insurgency that has claimed thousands of lives since emerging in 2012.
The failure fuelled frustrations with Keita's rule and tensions flared in April after the government held long-delayed parliamentary elections, the results of which are still disputed.
The Economic Community of West African States (Ecowas) last month suggested the formation of a unity government while offering continued support for Keita, but the compromise was slapped down by the opposition.
The 15-nation bloc -- which includes Mali -- also said that it would suspend the country from its internal decision-making bodies.
Further afield, Morocco on Wednesday stressed the need for "stability" in Mali, calling for "responsible dialogue, respect for constitutional order and the preservation of democratic gains."
Its campaign veered into crisis last month when 11 people were killed during three days of unrest sparked by a demonstration.
