The 47-year-old entered the competition under pressure, but managed to steer El Tri to a 10th Gold Cup title, and a record seventh in the tournament's current guise.
However, shortly after the team's 3-1 victory over Jamaica in the final, it was alleged that Herrera attacked a TV Azteca reporter in Philadelphia International Airport, resulting in renewed questions over his future.
Azteca subsequently released a statement saying: "We are surprised and concerned by the behaviour of the national team coach. The Mexican Soccer Federation should not allow attacks like the one suffered by our colleague."
The Mexican Football Federation have now decided to part company with Herrera following the incident, which the manager denies, claiming that he pushed the reporter rather than punched him.
"Violence has no place in society, family, and much less so in sport. Anyone who wants to use aggression and not the ideas and concepts based on freedom of expression cannot be a member of the Mexican Football Federation," read a statement from Decio de Maria, president of the Mexican Football Federation.
"Despite some extraordinary success during his coaching career, the results cannot rise above our statutes, regulations, respect and freedom of expression.
"The Mexican Football Federation, the different leagues that comprise it, and above all our national team should be an example to the younger generation and what happened does not show the spirit of fair competition we want to promote in our game."
Herrera's departure comes with just 10 weeks to go until Mexico face USA in a Confederations Cup playoff at the Rose Bowl.
Herrera guided El Tri to the last 16 of the 2014 World Cup, where they were beaten by Netherlands.