Talks are underway for the release of the other soldiers, said Togolese Foreign Minister Robert Dussey.
"I would like to announce that the President of the transition, President Assimi Goita of Mali, has agreed... to proceed with the release of some prisoners," Dussey told reporters in Togo's capital Lome.
He was speaking alongside Mali's foreign minister, Abdoulaye Diop, and Ivory Coast's cabinet director, Fidele Sarassoro.
The three Ivorian soldiers were present in uniform.
"Discussions are underway to ensure that the other soldiers in detention can very quickly regain their full freedom", Dussey added.
His country, "anxious to maintain good neighborly relations with Mali, undertakes to respect the procedures of the United Nations as well as the new Malian rules and provisions enacted concerning the deployment of military forces in Mali", he added.
The soldiers were arrested after their arrival at Bamako airport on July 10.
Ivory Coast says they were unfairly detained after being sent to provide backup for the UN peacekeeping mission in Mali, MINUSMA. They say their role within the mission was "well-known to the Malian authorities".
Mali's government however says they were detained after landing on a special flight without supporting documents and has described them as mercenaries.
In mid-August, Malian prosecutors filed charges against all 49 soldiers.
Public prosecutor Samba Sissoko on August 15 said the charges comprised "criminal association, attacking and plotting against the government, harming state external security, holding, carrying and transporting combat weapons and complicity in these crimes".
But negotiations continued, according to diplomatic sources, and Saturday's announcement appears to be the first concrete result from those talks.
Bamako also wanted Abidjan to hand over people who have been on its territory since 2013 who are wanted in Mali, said the sources in mid-August.
The junta has accused Ivory Coast of encouraging regional partners to impose harsh sanctions on Mali that were lifted in July.
Togolese President Faure Gnassingbe has been acting as a mediator in the dispute that sparked a diplomatic crisis between military-ruled Mali and its West African neighbour.
Ivory Coast "deplores the fact that shortcomings and misunderstandings were at the origin of this highly regrettable event", Sarassoro said at the news conference.
