The mission, known as MINUSMA, lowered the U.N. flag on its headquarters in the capital Bamako, its spokesperson Fatoumata Kaba told AFP.
The symbolic ceremony marks the official end of the mission, she said, even though some of the elements of it are still there.
A "liquidation phase" will take place after January 1, involving activities such as handing over remaining equipment to the authorities.
Mali's ruling junta, which seized power in 2020, in June demanded the departure of the mission, deployed since 2013, despite being in the grip of jihadism and raging crises.
The withdrawal of the U.N. stabilization mission, known as MINUSMA, has ignited fears that fighting will intensify between troops and armed factions for territorial control.
MINUSMA had for the past decade maintained around 15,000 soldiers and police in Mali. About 180 members have been killed in hostile acts.
As of Friday, more than 10,500 uniformed and civilian MINUSMA personnel had left Mali, out of a total of around 13,800 staff at the start of the withdrawal, the U.N. mission said on X, formerly Twitter.
Since being told to leave, MINUSMA has so far left 13 positions in Mali, and has yet to close sites in Gao and Timbuktu in the north.
Last week, the U.N. mission handed over the Mopti camp in the center of Mali, one of the hotbeds of jihadist violence that has plagued the Sahel region for years.
The Mopti camp most recently housed peacekeepers from Bangladesh and Togo, and in the past, hosted Egyptian, Pakistani and Senegalese contingents.
The pullout went smoothly, unlike recent withdrawals in Mali's volatile north which took place under fears of a military escalation between the army and rebel groups, Kaba told AFP.
Violence has swept the country while spilling over into neighboring Burkina Faso and Niger, inflaming ethnic tensions along the way.
After seizing power, Mali's junta ditched the country's alliance with former colonial power France, preferring rapprochement with Moscow.