Guzman, 56, was captured inside a condominium in the beach resort town of Mazatlan yesterday without a single shot being fired, ending a 13-year manhunt.
The US had offered a USD 5 million reward for information leading to the arrest of Guzman, whose Sinaloa cartel smuggled drugs over the Mexican border to America as well as to Europe and Asia.
Guzman, the billionaire head of the Sinaloa Cartel, was labeled "the godfather of the drug world" by US authorities.
Welcoming Guzman's arrest, US Attorney General Eric Holder praised Mexico for its "landmark" achievement and said it was a "victory for the citizens of both Mexico and the US."
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"We are pleased that we were able to work effectively with Mexico through the cooperative relationship that US law enforcement agencies have with their Mexican counterparts," Holder said.
"We look forward to ongoing cooperation, and future successes."
Holder's Mexican counterpart Jesus Murillo Karam said the arrest was the result joint operations with the US, which led to 13 arrests and the seizure of weapons that included 97 large guns, 36 handguns, two grenade launchers and a rocket launcher.
"We salute the government of Mexico, and the professionalism and courage of the Mexican authorities, for this arrest," he added.
Guzman had infamously escaped in 2001 from a high- security prison in a laundry cart.
The pressure on Guzman's organisation had been mounting for months with Mexican authorities killing or capturing several of its most brutal lieutenants, a US law enforcement official said.
Those operations yielded information, including cell phone and other data, that helped Mexican authorities and US drug enforcement agents track Guzman down.
Mexican government footage showed a handcuffed Guzman, with a dark mustache, being escorted by masked marines in Mexico City.