The Radisson Blu Hotel was stormed by special forces after gunmen entered it and seized 170 people.
Al-Qaeda in the Islamic Maghreb and its offshoot al-Murabitoun said they carried out the attack, according to an agency used by jihadists in the region.
Reporters have been told that at least 18 people have died in the siege and two of the gunmen have been killed.
One of those killed was Geoffrey Dieudonne, a member of parliament in Belgium’s Wallonia region.
Bamako-based journalist Francois Rihouay told the BBC that officials had said the operation was over, but during a live interview just before 17:00 GMT he heard shots being fired.
Security ministry spokesman Amadou Sangho told Reuters news agency that some of the gunmen were “dug in in the upper floors”.
“They are alone with the Malian special forces who are trying to dislodge them.”
Pictures show some of the hostages leaving the hotel were wounded; earlier, the interior minister said two soldiers had been injured.
The US-owned hotel is popular with foreign businesses and airline crews.
Eyewitnesses said the gunmen had entered the hotel shooting and shouting “God is great!” in Arabic.
Before special forces stormed the building, a security source told Reuters that some hostages who were able to recite verses of the Koran were being freed.
Mali’s presidency has tweeted (in French) thanking the security forces and friendly countries for their support in responding to the attacks.
Off-duty US servicemen helped in the hostage rescue operation. French special forces were dispatched to the scene.
There is as yet no established link with the attacks in Paris one week ago that killed 130 people.
In August, suspected Islamist gunmen killed 13 people, including five UN workers, during a hostage siege at a hotel in the central Malian town of Sevare.
France, the former colonial power in Mali, intervened in the country in January 2013, when al-Qaeda-linked militants threatened to march on Bamako after taking control of the north of the country.
Mali’s President Ibrahim Boubacar Keita has cut short a trip to a regional summit in Chad.
His French counterpart Francois Hollande said: “We should yet again stand firm and show our solidarity with a friendly country, Mali.”
The UN force in Mali took over responsibility for security in the country from French and African troops in July 2013, after the main towns in the north had been recaptured from the Islamist militants.