He was on the run for 181 days after his escape last July from a Mexican jail cell.
The first video of el Chapo in custody shows him with a towel on his head, Nubuck jacket and black pants.
Guzman was caught inside a private home following a shootout between Mexican commandoes and the drug kingpin's security staff. Five of his bodyguards were killed and one military officer wounded.
El Chapo and his crew had this arsenal at hand, including a rocket launcher. Six of his operatives were arrested during the takedown.
First word of the arrest came in a tweet posted by the president of Mexico: "Mission accomplished: we have him. I want to inform the Mexicans that Joaquin Guzman Loera has been detained."
Misión cumplida: lo tenemos. Quiero informar a los mexicanos que Joaquín Guzmán Loera ha sido detenido.— Enrique Peña Nieto (@EPN) January 8, 2016
Law enforcement sources say Guzman was tracked several days ago to the seaside town of Los Mochis on the Gulf of California, and that a citizen tip put him in the house where he was found, located in Mexico's Sinaloa region. Sinaloa is the namesake of Guzman's ruthless cartel, making it likely that during his 181 days of freedom he never ventured beyond his own territory.
Guzman is currently the lead defendant in a major drug prosecution in Chicago. He is also facing indictments in five other U.S. cities. There was a $5 million bounty on Guzman in handcuffs.
PHOTOS: See inside El Chapo's prison escape tunnel
While the arrest of el Chapo may ease the sting from his prison break last summer - his second in 15 years - the day's events were not completely successful. El Chapo's top deputy in northern Sinaloa, known as el Cholo Ivan, somehow managed to flee the scene and he is still a fugitive.
WHERE WILL EL CHAPO BE HELD?
When El Chapo tunneled his way out of a Mexican jail cell on July 11, American law enforcement officials were furious that the drug kingpin was able to escape. His disappearing act came just as the U.S. extradition request was winding its way through Mexican courts.
Now that he is back in custody, the question is: where will he be held?
In a chest-thumping statement late Friday afternoon, Mexico's president didn't mention the U.S. or extradition. His TV speech heralded the effort to recapture el Chapo in his home district.
A few hours later, in custody, el Chapo was transported under military guard to a nearby airport where he was seen being put onto a jet-destination unknown.
"There are really two kinds of battles going on: one is between the United States and Mexico for who has the rights to try him in the first place and the second is who within the United States - which jurisdiction - can try him first. And Chicago has a pretty good claim on him because he's responsible for a lot of drug traffic in Chicago," said Gil Soffer, former federal prosecutor.
"The justice department makes the decision based on where are the facts strongest? Where can we bring our best case? Where are the witnesses located? Which sets of prosecutors are best able to bring this kind of action? There's a whole set of factors to consider," Soffer said.
ABC7's Chuck Goudie: "One year from now, presuming he hasn't escaped again, what's your best guess as to where el Chapo will be?"
Soffer: "Pure speculation, my guess is - for mostly political and not legal reasons - he will still be in Mexico."
The U.S. Attorney General and Drug Enforcement Administration both put out statements late Friday concerning el Chapo, neither mentioning extradition, although it is believed that the Department of Justice will submit a renewed extradition request with the hope that they can restart the process as soon as possible.