"There are 12 dead in all," an army officer told AFP after the operation at the Hotel Byblos in Sevare, listing the fatalities as five "terrorists", five soldiers and two "white people".
The body of one of the foreign victims had lain in front of the hotel since Friday when the gunmen stormed the building, the officer said.
South Africa's foreign ministry said a 38-year-old man from Pretoria was killed in the siege while two other South Africans were safe.
A source told AFP that "a number of hostages" had been freed from the hotel, including five foreigners, although their nationalities were not specified.
UN chief Ban Ki-moon condemned the attack which "led to the death of at least one UN contractor," his spokesman said in a statement.
"This attack will not lessen the determination of the United Nations to accompany the Malian people in their efforts to implement the peace agreement," the statement said, referring to the UN peacekeeping mission MINUSMA.
Sources said three South Africans, a Frenchman and a Ukrainian had been registered at the hotel at the time of the attack. A Russian diplomat said a Russian was among the hostages.
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