The Radisson Blu hotel chain said two armed men locked in 140 guests and 30 employees, CNN reported.
The victims comprised two Malian citizens and a French national, authorities said.
The armed men came in a diplomatic vehicle earlier in the day, firing as they entered the hotel, said witness Amadou Keita, who works at a cultural centre nearby.
The firing went on for several minutes, he said.
Malian soldiers with help from UN troops surrounded the hotel.
No group immediately claimed responsibility for the incident.
The Radisson Blu hotel is about 15 minutes away from Bamako Senou International Airport.