Five suspected jihadists have been placed in custody while four attackers were killed at the scene, Security Minister Salif Traore told AFP.
He said 36 mostly French and Malian hostages were freed following the incident at the Kangaba Le Campement resort yesterday afternoon.
Speaking in Luxembourg, EU foreign affairs chief Federica Mogherini said the two EU staff victims were a Malian woman and a Portuguese man.
Around 20 members of Mali's special forces remained at the ecolodge today, Traore added, continuing investigations at a destination known for its popularity with expatriates on weekends.
Some of the assailants had shouted "Allahu Akbar" - Arabic for 'God is greatest' - other witnesses interviewed by AFP said. So far, no group has yet claimed responsibility.
Meanwhile a Kangaba employee described ushering clients into a hiding place, a possible explanation for the relatively low death toll compared with the lives lost in previous assaults on tourist targets in west Africa.
Domestic and foreign forces deployed in Mali's troubled north and centre have been repeated targets of jihadist forces, but attacks on civilians in and around the capital are rare, with the last major incident in November 2015 when gunmen stormed the Radisson Blu hotel.
That attack, which killed 20 people, caused the government to call a state of emergency which has been in place more or less ever since.
Among those saved yesterday were two Spaniards, two Dutch and two Egyptian nationals, according to Mali's security ministry.
Earlier this month, the US embassy in Bamako had warned about "a possible increased threat of attacks against Western diplomatic missions, places of worship" and other places frequented by Westerners in Bamako.
Back in January, the Kangaba's owner, Herve Depardieu, had complained about the "alarming security information" issued by foreign consulates.
Yesterday's attack is the latest in a series of high- profile assaults in north and west Africa targeting locals and tourists, including in neighbouring Burkina Faso and Ivory Coast.
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.
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