The attack against the ELN was carried out near the border with Venezuela and took place the day after US President Donald Trump received Colombian President Gustavo Petro at the White House.
The two leaders then agreed to cooperate - militarily and with intelligence - to combat drug trafficking and three prominent drug lords in Colombia.
US forces were not involved in Wednesday's attack, according to the Colombian military.
The militant leftist ELN, which emerged in the mid-1960s, is one of the last guerrilla movements active in Latin America. It controls large areas of Colombia where drugs are produced.
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