His arrest capped a months-long operation that resulted in the arrests of a dozen Sinaloa cartel operatives, including alleged bodyguards of Guzman's top associate, Ismael "El Mayo" Zambada.
Several cellphones were seized from the detainees and later used to establish wiretaps as part of the operation against the Sinaloa cartel, said an official from the Mexican attorney general's office.
The official said authorities are still searching for Zambada, who is considered Guzman's natural successor.
Nabbing Guzman, who is considered the world's biggest drug trafficker, was a major victory in President Enrique Pena Nieto's push to rein in drug violence in his country. The Sinaloa cartel's turf wars with rival gangs contributed to a wave of drug violence that left more than 77,000 people dead in the past seven years.
The United States had offered a $5 million reward for information leading to his capture, with several indictments in cities from New York to San Diego. Robert Nardoza, a spokesman for the US Attorney's Office for the Eastern District of New York, said prosecutors there "plan to seek his extradition."
A senior Republican lawmaker called for Guzman's extradition, warning that "the biggest fish ever" may try to flee again in a repeat of his legendary 2001 escape from prison in a laundry cart.
"I think that would be the best course for not only Mexico, but also the United States, in ensuring that what happened in 2001 does not happen again," Michael McCaul, chairman of the House Homeland Security Committee, told ABC television.
A Mexican foreign ministry spokesman declined to comment on the planned extradition request. An official in the Mexican attorney general's office said Guzman has to finish the 20-year sentence he avoided by fleeing eight years into his prison term.
But he is also facing new charges of drug trafficking, using illegal funds, organized crime and possession of weapons reserved for the military, the official said. The captured kingpin is not facing murder charges.