Ibrahim Traore becomes interim president and warns in a speech the West African country is "confronted with a security and humanitarian crisis without precedent."
The seizure of power by some military leaders on Friday marked Burkina Faso's second coup this year.
Major regional groups have called upon the new military leadership to ensure that the constitution is restored by July 2024.
More than a dozen members of Burkina Faso's army seize control of state TV, declaring the country's coup leader-turned-president Paul Henri Sandaogo Damiba, has been overthrown.
Emergency talks were triggered after Burkina Faso became the third member of the ECOWAS to be overtaken by the military in less than two years.
The bloc's 15-member Peace and Security Council has voted to suspend the participation of Burkina Faso in all African Union activities "until the effective restoration of constitutional order in the country."
The leaders previously issued a statement to say the bloc "firmly condemns" the coup, accusing the military of forcing Kabore to resign "under threat, intimidation and pressure".
African and Western powers denounce what they called an "attempted coup" and the EU demands "immediate" release of President Roch Marc Christian Kabore.
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