The governor of Jalisco, Pablo Lemus Navarro, on social media advised residents of the state to adhere to a code red warning and avoid leaving their homes.
The US State Department also issued a shelter-in-place warning for US citizens in Jalisco State, Tamaulipas State, and areas of Michoacan State, Guerrero State, and Nuevo Leon State.
The Mexican defence ministry said the US had supplied Mexico with information that assisted its operation.
Former US ambassador to Mexico and Deputy Secretary of State Christopher Landau said on social media that El Mencho’s death was “a great development for Mexico, the US, Latin America, and the world”.
The US had previously offered a $15m (£11.1m) reward for information leading to El Mencho’s capture.