The dismissal of Lieutenant-Colonel Paul-Henri Sandaogo Damiba, who himself came to power in a coup last January, was announced in a statement read out on national television.
The rebelling military also announced the closure of borders from midnight, as well as the suspension of the constitution and the dissolution of the government.
They declared the country's new strongman as Captain Ibrahim Traore.
Around 15 soldiers in fatigues appeared on the Radio-Television broadcaster shortly before 8:00 pm local time and read out the statement.
"We have decided to take our responsibilities, driven by a single ideal — the restoration of security and integrity of our territory", they said.
A curfew from 9:00 pm to 5:00 am was also announced.
Earlier on Friday, the government said an "internal crisis" within the army was behind troop deployments in key areas of the capital, and said negotiations were underway after shots rang out before dawn.
Residents who live close to the presidential palace reported hearing heavy detonations in the morning.
“I heard heavy detonations around 4:30am and now the roads around my home have been sealed off by military vehicles,” said the resident.
Burkina Faso, Mali, Chad and Guinea have all experienced military coups since 2020, a development which raises fears of backsliding towards military rule in the region that has made democratic progress in recent decades.
