Chairing the meeting, Simeon Oyono Esono, Equatorial Guinea permanent representative to AU, told reporters that the meeting of the council deliberated on the crisis in the West African nation.
He said the council has called for transfer of power to civilians in two weeks period otherwise the country would face sanctions.
The change in Burkina Faso has been against democracy, he said.
"However, we know that the popular pressure led to the resignation of the president. We have taken note of the origin of the popular revolt which led to the military to get into power. So, we determined the period of two weeks and after that period we are going to apply sanctions," he noted.
"After the armed forces relinquish power, we are going to designate a new envoy which is the ex-prime minister of Togo to examine the situation from the field and we are going to meet again in the Council to examine and to see the steps to be followed."
Nkosazana Dlamini-Zuma, chairperson of the AU Commission, called on the political stakeholders and civil society in Burkina Faso to work together in a spirit of consensus and responsibility, in order to agree on a civilian-led transition that would culminate, as soon as possible, in the holding of free, fair and transparent elections.
The chairperson underlined that a civilian-led and consensual transition would not only be consistent with the legitimate aspirations of the people of Burkina Faso for change and the deepening of democracy, but would also facilitate the mobilisation of the support necessary for a successful way out of the crisis.