Hernandez Manrique died in the city of Segovia, military spokesmen said.
A man accompanying the rebel commander was wounded in the operation, press reports said.
Hernandez Manrique was in command of ELN units in Antioquia and Bolivar provinces, overseeing 13 units, Caracol Radio reported.
The rebel commander was the target of an intelligence operation that took several months to develop and was killed by army special forces members.
The government and the ELN, Colombia’s second-largest guerrilla group, started exploratory talks for a peace process in January 2014 in Havana, but the dialogue has not led to negotiations like those between Bogota and the Revolutionary Armed Forces of Colombia, or FARC.