The soldiers were surrounded by hundreds of people as they went to arrest a man wanted for homicide and illegal firearm fabrication, the army had said.
The man was injured while trying to escape, and the Indigenous community of Toribio in the Cauca department accuse authorities of maltreating him.
The community took hostage more than a dozen soldiers, with video footage on social media showing them being led away in single file surrounded by members of the Indigenous guard, an unarmed organization that defends the community's interests.
The army -- which had earlier put the number of soldiers taken at 16 -- said it would file a complaint for "kidnapping and riot" against the hostage takers.
On Wednesday the ombudsman's office said all 17 soldiers taken by the community had been released. They said they had been treated well.
Indigenous people in Colombia often kidnap security forces personnel as a method of protest.
In early March, a community in the southwest took 80 police members hostage for two days in protest against the activities of an oil company.
Ensuing clashes between protesters and security forces left one villager and one police officer dead.
Colombia has suffered decades of a multi-faceted armed conflict involving drug traffickers, left-wing guerrillas, right-wing paramilitaries and security forces.
Indigenous people have often been the victims in the conflict, which has left nine million people either dead, injured or displaced.
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