"I congratulate our Public Forces for neutralizing Alvaro Gelves Ortega, alias Jairo, 1st leader of the ELN's Jose Antonio Galan Front," Santos wrote on Twitter.
The operation, which took place in the south of the country's northern Bolivar department, also left Ortega's "escort" dead, according to a tweet from General Jorge Nieto, director of Colombia's National Police.
The authorities did not provide further details regarding the operation.
The leftist National Liberation Army (ELN) and the Santos government have been engaged in rocky peace talks since February.
Santos is trying to achieve "complete peace" by seeking a deal with the ELN without a ceasefire in place.
Colombian authorities say the multi-sided conflict has killed 260,000 people, left 60,000 missing, and displaced 6.9 million since it started with a leftist uprising in 1964.