The kingpin rose to prominence as a co-founder of the Guadalajara cartel, one of Latin America's most powerful drug trafficking organisations during the 1980s, and had been among the most prized targets for US officials.
Caro Quintero spent 28 years in prison for the brutal murder of former US Drug Enforcement Administration (DEA) agent Enrique 'Kiki' Camarena.
It was one of the most notorious murders in Mexico's bloody narco wars that led to a nadir in US-Mexico co-operation in the five-decade long 'war on drugs'.
The events were dramatised in the 2018 Netflix series Narcos: Mexico.
Caro Quintero has previously denied involvement in the killing of Camarena.
In 2013, Caro Quintero was released on a technicality by a Mexican judge.
He quickly went underground and returned to trafficking, according to US officials, who placed him on the FBI's Top 10 most-wanted fugitives list and put a $US20 million ($A29 million) bounty on his head, a record for a drug trafficker.
"It is probably one of the most important captures of the last decade in terms of importance to the DEA," Mike Vigil, the DEA's former chief of international operations, said.
While Caro Quintero is no longer considered a major player in the international drug trafficking world, the symbolic impact of his capture is likely to be significant on both sides of the US-Mexico border.
"This will hopefully start to mend the frayed relationship between the United States and Mexico in terms of combating drug trafficking," Vigil said.
Mexico's unwillingness to extradite Caro Quintero to the United States prior to his release from prison had been a source of tension between the two countries and Washington is likely to demand his extradition once again.
Last year, Caro Quintero lost a final appeal against extradition to the United States.
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