Bamako has been on high alert since a heavily armed gunman burst into La Terrasse, a popular venue among expatriates, on Saturday and killed five people, including a French national, a Belgian and three locals.
"During an operation launched today, one of the perpetrators of the terrorist crime last Saturday was killed. He did not want to surrender," a senior special forces commander told AFP.
"We located the individual in a popular district of Bamako. He is from the north. He had shaved his head," said another special forces source who told AFP he had taken part in the operation.
"He is one of Saturday's attackers. He was the one who launched a grenade from his motorbike into the street outside the La Terrasse restaurant-bar," he said.
Around a dozen people were arrested, security sources said, while three special forces personnel were slightly wounded.
The operation marked a dramatic twist almost a week after the attack, in which eight people - two of them Swiss nationals - were wounded.
Sources have spoken of a number of leads, including clues on the getaway vehicle and its driver, but investigators had made no announcements of substantial progress in the hunt for the killers before today's operation.
Officers found an identity card on the dead suspect purporting to belong to a man in his early 20s born in the village of Moudakane, near Gao, northern Mali's largest city, sources told AFP.
Al-Murabitoun, a jihadist group run by leading Algerian militant Mokhtar Belmokhtar, has claimed responsibility for the nightclub assault.
The group said it had struck partly to avenge Ahmed el Tilemsi, one of its commanders killed by the French army in Mali in December.
But it added that the attack was mainly a response to recent cartoons of the Muslim prophet Mohammed, "whom the miscreant West insulted and mocked.