Police reportedly tracked the pair, said to be from the group's southern wing, for 15 days before seizing them.
Fighters from the Revolutionary Armed Forces of Colombia (Farc) have been known to cross Colombia's border into neighbouring countries in order to hide from the military.
Last month's raid killed about 20 Farc fighters, including one of the group's main leaders, Raul Reyes.
Ecuador and Venezuela responded by cutting diplomatic ties with Colombia and sending troops to their borders with the country.
The crisis was resolved earlier this month at a summit of Latin American leaders in the Dominican Republic.
Colombia apologised for the raid but said it had been necessary in order to combat the Farc group, which has waged a decades-long war against the government.
The Organisation of American States also "deplored" the incident.