Dairo Antonio Úsuga, better known as Otoniel, was seized after a joint operation by the army, air force and police on Saturday.
The government had offered a $800,000 (£582,000) reward for information about his whereabouts, while the US placed a $5m bounty on his head.
President Iván Duque hailed Otoniel’s capture in a televised video message.
“This is the biggest blow against drug trafficking in our country this century,” he said. “This blow is only comparable to the fall of Pablo Escobar in the 1990s.”
Otoniel was captured in his rural hideout in Antioquia province in north-western Colombia, close to the border with Panama.
The operation involved 500 soldiers supported by 22 helicopters. One police officer was killed.
Otoniel had used a network of rural safe houses to move around and evade the authorities, and did not use a phone, instead relying on couriers for communication.
But his location at the time of his capture was pinpointed two weeks ago, El Tiempo newspaper said.
Police chief Jorge Vargas said his movements were traced by more than 50 signal intelligence experts using satellite imagery. US and UK agencies were involved in the search.
Mr Duque, quoted by AFP news agency, described the operation as “the biggest penetration of the jungle ever seen in the military history of our country”.
Colombia’s armed forces later released a photo showing its soldiers guarding Otoniel, who was in handcuffs and wearing rubber boots.
There have been several huge operations involving thousands of officers to capture the 50-year-old in recent years, but until now none have been successful.