The French and Ivorian defence ministers signed a document to confirm the return, shortly after the Ivorian flag was raised in the base's parade ground.
Though the handover comes as a spate of France's former colonies in west Africa weaken ties with their former ruler, both sides stressed that relations remained warm.
"This act marks a new era in the friendship and strategic collaboration between our two countries," Ivorian Defence Minister Tene Birahima Ouattara said.
His French counterpart Sebastien Lecornu said that as "the world is changing... it's obvious that our military relationship should change".
Lecornu hailed the base's handover as a "historic moment" for the two countries, who share "a relationship built on friendship and a high level of professionalism".
"The presence of France is changing, but not disappearing," he said.
Ouattara also said he wanted to "reassure" France that military cooperation between the two countries would be "as good as it has always been" in the future.
After the ceremony, Lecornu met with Ivorian President Alassane Ouattara.
"This is not a clean break, it's another way of collaborating -- based on training, equipment and tackling drones", a source from the Ivorian president's office said. The two officials discussed international matters during their meeting, particularly Ukraine.
A changing of the guard took place at the beginning of the ceremony to mark the transfer of security responsibilities to the Ivorian army.
In the last few weeks, around 100 Ivorian paratroopers have also moved into the camp, and joint exercises took place between the two armies.
- Sovereignty -
About 1,000 French soldiers were deployed in Port-Bouet and helped in the fight against jihadists, who launch regular attacks across the wider region.
Ivory Coast has remained an anomaly in France's relationship with Africa, maintaining links with its former colonial power since its independence in 1960, despite a decade of crisis in the 2000s.
Elsewhere in the region France is revamping military relations with African nations after the forced departure of its troops from Mali, Burkina Faso and Niger, where military-led governments hostile to Paris have seized power.
In November, Senegal and Chad also announced within hours of each other that they would bring France's military presence in their countries to an end.
Many of those governments have stressed the importance of sovereignty and questioned the need for France's continued presence in their countries.
"The Ivorian authorities know very well that there is support for sovereignty in the country, so the French military departure is something that should happen before it becomes a mainstream demand", Ivorian political analyst Geoffroy Kouao told AFP.
- 'Valued partner' -
The French withdrawal will take place gradually over the course of 2025, but around 80 French soldiers are expected to remain for training and support missions.
"Paris will remain a valued partner in training, intelligence and especially in the fight against terrorism", Geoffroy Kouao said.
The 230-hectare (570-acre) Port-Bouet military camp flanking Ivory Coast's largest city of Abidjan has been a fixture in the country's life since 1978 and helped stabilise the world's top cocoa producer after coups and unrest broke out in the nation after the turn of the millennium.
In 2002, following an attempted coup against then-president Laurent Gbagbo and the takeover of part of the country by rebels, France put in place the Licorne (Unicorn) force to protect French nationals and to try to stabilise the country.
In April 2011, this force, alongside the United Nations, carried out bombings on Gbagbo's residence, after several months of post-election crisis.
The mission wound up in 2015.
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