Fighting broke out in Timbuktu over the weekend after Islamists attempted to infiltrate Mali's liberated northern city, DPA reported.
According to Mali army spokesman Souleymane Dembele, an exchange of fire took place late on Saturday, after a "jihadist vehicle attempted to force its way through a checkpoint" and then exploded.
Two Islamists were killed and injuries were reported among the soldiers after an attempt to occupy an abandoned military camp, the spokesman said.
Witnesses contacted by dpa spoke of a third body at the scene.
The latest fighting comes about 10 days after a suicide car bomber killed a Malian soldier and wounded several others in the historic city. That was the first such attack in the city since French and Malian forces retook control of Timbuktu from Islamist rebels some two months ago.
Earlier this week, President Francois Hollande confirmed his determination to reduce the presence of French troops in Mali by half by July.
That would mean a drop from the current 4,000 French troops in the troubled West African country to 2,000.