Burkina Faso's new military leader, Capt Ibrahim Traoré has confirmed receipt and acceptance of the resignation of Lt Col Paul-Henri Damiba's, who was ousted in a coup last week on Friday.
Traoré led the coup in the west African country on Friday.
The announcement followed attacks on French institutions, after it was reported that Damiba was being sheltered at a French military base.
Unconfirmed reports say he is in Togo, according to Reuters.
Pro-Russian slogans were chanted and Russian flags waved by supporters of the new coup leader Traoré on Sunday.
He regards former colonial power France as an ally of the man he ousted, and has spoken of his willingness to work with new partners to fight Islamist insurgents - and analysts believe that could mean hiring Russian mercenaries.
Burkina Faso controls as little as 60% of its territory, and the situation is only worsening, reports indicate.
On Sunday, Traoré said the country was facing an emergency in every sector, and ordered cabinet ministers to "move faster and abandon the unnecessary red tape".
The African Union has demanded the return of constitutional order by July 2023 at the latest, agreeing with the regional group Economic Community of West African States (Ecowas) that the ousting of leader Damiba was "unconstitutional".
But Ecowas has since praised "the various parties in Burkina Faso for agreeing to a peaceful settlement of their differences", as days of power struggles came to an end without bloodshed.
No statement has been released by Damiba directly.
But religious and community leaders said Damiba himself had offered his resignation "in order to avoid confrontations with serious human and material consequences," according to sources cited by AFP news agency.
They said Damiba had set seven conditions for stepping down - including a guarantee of his security, an agreement to continue with efforts at national reconciliation and a continued respect for the guarantee of returning to civilian rule within two years.
The ousted colonel had also previously led a coup to depose President Roch Kabore in January, on grounds that he had failed to deal with growing militant Islamist violence.
This is Burkina Faso's ninth coup since independence from France in 1960.