Vice president Assimi Goita, who led the August coup, dismissed president Bah N'Daw and prime minister Moctar Ouane for naming a new government without consulting him, Bloomberg reported.
The pair were detained in army headquarters, prompting an outcry from international leaders.
"We call for their immediate, unconditional release," the US State Department's Bureau of African Affairs tweeted.
In a translated statement on Twitter, French president Emmanuel Macron said the coup d'etat was "unacceptable".
"We are ready to take targeted sanctions on the protagonists," he said.
Goita said a new interim government would be named and presidential elections would be held in February, Bloomberg reported.
London-based SP Angel played down the developments.
"The actions of the military in Mali are not overly unusual and often serve to restore order and stability," the broker said in a morning note.
Mining is a key driver of Mali's economy.
Miners operating in Mali include Canada's Barrick Gold and B2Gold and Australia-based Resolute Mining and Firefinch.
Firefinch (ASX: FFX), which operates the Morila gold mine in Mali, lost 15% yesterday but was up 4% in midday trade.
Resolute lost about 6% yesterday in both Australia and London. Its Australian-quoted shares (ASX: RSG) were flat at the time of writing.
B2Gold (TSX: BT0) closed down 3.1% yesterday and Barrick was off 0.5% in Toronto.