Hernandez, 44, was also known as "the Condor" and he was a top figure in the Juarez cartel, the BBC reported.
He was killed Tuesday, but he was holding false papers, which delayed his identification, the Chihuahua state prosecutors' office said. He is accused of being involved in nearly 100 murders.
Three alleged associates were captured and taken to Mexico City for questioning. The Juarez cartel controls many of the drug smuggling routes from Mexico to the United States.
Authorities said the Juarez cartel is responsible for many of the executions and decapitations in the border town of Juarez, which had more than 3,000 homicides in 2010.
Police said the Juarez cartel and the rival Sinola cartel are responsible for much of the drug violence in Chihuahua.
There have been more than 34,000 drug-related killings in Mexico since President Felipe Calderon started cracking down on drug cartels in late 2006.