The assault on the Kangaba Le Campement resort comes after a similar strike less than two years ago on a luxury hotel in Bamako, which lies in the south of the troubled country.
Security forces who battled the gunmen at the site were continuing Sunday evening to search for the assailants who fled.
Nearby residents had first reported the attack after hearing shots while smoke billowed into the air, with at least one building ablaze.
"Unfortunately for the moment there are two dead, including a Franco-Gabonese," he said, adding that the second body was being identified.
At least "32 hostages" were freed, Mali's army said in a statement, adding that one of the attackers was wounded and gave up his weapon. He also left behind "bottles containing some explosive substances", the security ministry said.
At least 14 people, both Malians and foreigners, were injured, according to the ministry.
The landlocked west African country has been fighting a jihadist insurgency for several years, with Islamist fighters roaming the north and centre of Mali.
French President Emmanuel Macron, who is scheduled to visit Bamako on July 2 for a meeting with five Sahel countries, "is following the situation very closely," the presidency told AFP yesterday.
Several people rescued at Kangaba said assailants had shouted "Allahu Akbar (God is Greatest)", although no group has yet claimed responsibility.
At a France-Africa summit in Bamako in January, the owner of Kangaba, Herve Depardieu, had complained about the "alarming security information" given by foreign consulates "which seriously disturb our love of life and our freedoms".
In November 2015, gunmen took guests and staff hostage at the luxury Radisson Blu hotel in Bamako in a siege that left at least 20 people dead, including 14 foreigners.
That attack was claimed by Al-Qaeda's North African affiliate Al-Qaeda in the Islamic Maghreb (AQIM).
The Kangaba, located on the eastern edge of Bamako, boasts accommodation in hut-style rooms, as well as restaurants and swimming pools, according to its website.
A state of emergency has been renewed several times since the Radisson Blu attack, most recently in April when it was extended for six months, but attacks are continuing.
In 2012 Mali's north fell under the control of jihadist groups linked to Al-Qaeda who hijacked an ethnic Tuareg-led rebel uprising, though the Islamists were largely ousted by a French-led military operation in January 2013.
The unrest has continued despite a 2015 peace deal between the government and Tuareg-led rebels offering partial autonomy to the north.
Sunday's attack is the latest in a series of high-profile assaults in north and and west Africa, targeting locals and tourists.
In January 2016, 30 people were killed, including many foreigners, in an attack on a top Burkina Faso hotel and a nearby restaurant in the capital Ouagadougou. AQIM claimed the assault, saying the gunmen were from the Al-Murabitoun group of Algerian extremist Mokhtar Belmokhtar.
The United Nations has a 12,000-strong force in Mali known as MINUSMA, which began operations in 2013.
It has been targeted constantly by jihadists, with dozens of peacekeepers killed, including five on Saturday.
France also has 4,000 soldiers in its Bakhane force in five countries -- Mali, Mauritania, Niger, Chad and Burkina Faso -- all of which are threatened by the jihadists across their porous borders.
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