Dairo Antonio Usuga, known as Otoniel, was caught by Colombia's armed forces during an operation in a rural area of Colombia's Uraba region, Antioquia province, which involved more than 500 members of Colombia's special forces and 22 helicopters, officials said on Saturday.
Otoniel is accused of exporting hundreds of tonnes of cocaine each year, while President Ivan Duque said on Saturday he is also responsible for killing police officers, recruiting minors and sexually abusing children.
Colombia's government will file a petition on Monday with the Andean country's Supreme Court to extradite Otoniel to the United States, Justice Minister Wilson Ruiz told Reuters on Sunday, adding the process could take four weeks to complete.
"Extradition awaits all those who commit international crimes," Defence Minister Diego Molano told journalists in Necocli, close to where Otoniel, 50, was captured.
Colombia had offered a reward of up to 3 billion pesos (about $800,000) for information concerning Otoniel’s whereabouts, while the US government had put up a reward of $5 million for help locating him.
Both rewards will be paid, Molano said, while describing Otoniel as "the worst kind" of criminal.
Otoniel rose to become the leader of the drug-trafficking group Clan del Golfo, or Gulf Clan, following stints as a left-wing guerrilla and later as a paramilitary.
The Clan del Golfo has a presence in 12 of Colombia's 32 provinces, and counts some 3,800 members, according to information provided by Colombia's national police.
Clan del Golfo is involved as well with illegal mining, authorities say. The government also accuses the group of threatening and killing community leaders across the country.
Colombia's police chief, General Jorge Vargas, said much of the information leading to Otoniel's capture came from Clan del Golfo members.
"A lot of Clan del Golfo's people betrayed him," Vargas said.
Otoniel trafficked between 180 tonnes and 200 tonnes of cocaine a year with the Clan del Golfo, and is responsible for the deaths of more than 200 members of Colombia's security forces, the Defence Ministry said in a statement.
Colombian authorities launched Operation Agamemnon in 2016 as they worked to close in on Otoniel, killing and capturing dozens of his lieutenants, going after his finances and forcing him to be constantly on the move, according to police.
In 2017, a video in which Otoniel announced his intent to submit to justice was published, but the plan never came to fruition.