The French force which has been present in the West African Country since 2013, leaves the country after a public fallout with the new Military Junta Government in Mali.
The new regime has blamed France for being at the center of division amongst Malians.
Speaking in Brussels on Thursday, Macron said the EU and France no longer share the same priorities with the government in Mali.
“We cannot remain militarily committed with authorities to which we do not share same priorities,” Macron said.
He also paid tribute to the soldiers who died in Mali, while fighting terrorism in the region. About 48 French soldiers are reported to have died in Mali.
France has a little over 4,000 soldiers in the Sahel, with most of them stationed in Mali.
Macron says most of them will now be redeployed to other countries within the Sahel, where the EU and its African fighters are fighting al-Qaeda and Daesh terrorists.
Macky Sall, the president of Senegal and the chair of the African Union, expressed his gratitude to the EU and agreed with the move to withdraw from Mali.
Nana Akufo-Addo, who represents the ECOWAS, said Africa has to keep up the fight against terrorism, he added that Africa “cannot let terrorists stay in Africa, after being chased from middle east and Afghanistan”.