Vicente Carrillo Fuentes, known as "the Viceroy", was held in the northern city of Torreon.
The arrest is the latest in a series of high profile operations against drug lords in Mexico this year.
He is said to have waged war with the rival Sinaloa gang over control of trafficking routes to the US.
The war left thousands dead in and around Ciudad Juarez on the border with the United States between 2009 and 2011.
The US had offered a reward of $5m for his arrest.
Vicente Carrillo Fuentes took over the cartel from his brother Amando, nicknamed "Lord of the Skies", who died in 1997 after a botched cosmetic surgery operation.
Amando got his nickname by flying planeloads of drugs into the US, but his brother Vicente carried on trafficking on a more modest scale.
Despite recent news reports about its decline, the Juarez Cartel remains one of the most powerful criminal organisations in Mexico and the region.
The cartel maintains a firm foothold in Ciudad Juarez and the Valle de Juarez, which remains the key corridor for transporting illegal drugs into the US.
Correspondents say it still has some measure of control over the local and state police, as well as some politicians.
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