After the soldiers engaged in fierce clashes with the guerrillas on Monday, local villagers blocked roads to prevent the departure of the troops -- an act that the leftist government of Gustavo Petro deemed a kidnapping.
"At this moment, soldiers are withdrawing from the village Nueva York" in the Guaviare province, Iris Marin, head of the Ombudsman's office, said on X.
"We urge people not to stigmatize the community," Marin added.
Delegations from the government, the Ombudsman's office and the United Nations mediated the release of the soldiers.
The authorities initially reported that 34 soldiers had been detained, but later revised the number down to 33.
The mass detention of troops has become commonplace in southern Colombia.
According to the government, such detentions are often carried out by local people who are being manipulated by armed groups in areas where there is little state presence.
The clashes between the soldiers and armed rebels led by warlord Ivan Mordisco began on Sunday, leaving 10 dead.
The defense ministry said on social media that it had filed a complaint about the kidnapping to the public prosecutor's office.
The army sent in "more troops to prevent any attacks in this hostile environment" where the local population "is being manipulated" by the rebels, according to a statement from military commander Admiral Francisco Cubides.
Colombia has been enduring rising violence from dissident groups who rejected a 2016 peace agreement with the bulk of the Revolutionary Armed Forces of Colombia (FARC) after a six-decade-long insurgency.
Last week, another group under Mordisco's command detonated a truck bomb that killed six people and wounded more than 60 in the southwestern city of Cali.
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