The cartel leader died after being wounded in a firefight between his bodyguards and Mexican special forces personnel deployed to capture him in late February. BBC reported.
The 59-year-old founder of the feared Jalisco New Generation Cartel (CJNG) was the country's most-wanted man, while the US had offered a $15m (£11.2m) reward for information leading to his arrest.
His death triggered widespread retaliatory violence in which cartel members set fire to vehicles and blockaded roads across 20 Mexican states.
Members of the National Guard were out in force to prevent fresh violence from breaking out during the colourful funeral near Guadalajara in Jalisco state, a stronghold for the cartel.
Large floral tributes were seen being carried into the funeral home ahead of the ceremony, including one shaped like a rooster in a reference to his love of cockfighting.
