"The rebel known as Marquitos, leader of the ELN's Dario Martinez front and a member of its national leadership, has been killed. Congratulations, armed forces," President Juan Manuel Santos said in a message on Twitter, posted while traveling in Rome.
The death of the rebel, whose real name is Jose Amin Hernandez, was a "decisive blow" to the ELN thanks to an operation by the police and armed forces, an Army statement said.
Amin Hernandez was also blamed for the 1999 hijacking of a domestic flight with 46 people on board, AFP reported.
The ELN, with about 2,500 guerrillas, is Colombia's second largest insurgent group. It currently is not part of ongoing peace talks with the government.
The Colombian conflict has killed more than 200,000 people and uprooted more than six million since the Revolutionary Armed Forces of Colombia (FARC) was launched in 1964.
Peace talks in Havana between the FARC and the Colombian government have produced partial deals on several issues, including ending the drug trafficking that has fueled the conflict. But they have yet to reach a final accord.