The putsch was announced after the presidential guard stormed a cabinet meeting detaining the interim president and prime minister.
A close ally of ex-President Blaise Compaore has been named the new leader.
The US, France and the African Union (AU) have condemned the takeover in the former French colony.
Elections were due to be held on 11 October nearly a year after a popular uprising forced Mr Compaore, the long-time ruler of the West African country, from power.
The headquarters of Mr Compaore’s Congress for Democracy and Progress (CDP) party were ransacked in Ouagadougou as news of the coup spread, the AFP news agency reports.
The AU and regional body the Economic Community of West African States (Ecowas), called for the immediate release of “hostages”, referring to interim President Michel Kafando and Prime Minister Isaac Zida, who were detained at a cabinet meeting in the president palace on Wednesday.
President Sall said he was heading to Ouagadougou in his role as the current chairman of Ecowas.