Corona - capped by his country 12 times - was caught by TV Azteca cameras head-butting Morelia physical trainer Sergio Martin during the fracas, resulting in a six-match suspension by the Mexican Football Federation.
"We have decided not to take Jesus Corona to the Gold Cup. We have called up Jonathan Orozco (of Monterrey in his place)," Femexfut's national teams director Hector Gonzalez said.
With Morelia leading 3-0 in the 89th minute and 3-2 on aggregate, one of their fans ran onto the pitch, made a remark to Crux Azul captain Gerardo Torrado and was attacked by several of the visiting team's players, sparking a free-for-all.
The referee dismissed three players, two from Cruz Azul and one from Morelia, and sent both teams' coaches to the stands but missed the incident involving Corona.
"One works to be first choice in the team and get to the Tri (Color). It's lamentable what happened," Corona told reporters. "I make a little mistake and I'm out of the national team.
"I'm upset, I lost control and assume my responsibility (but) I'd like to talk to the federation directors to give my story of the reaction."
It is the second time in a year that Corona has been dropped from the national side because of his behaviour. He was left out of their 2010 World Cup squad for hitting a person on a bar.
Morelia meet Pumas UNAM, who overcame Guadalajara 2-0 for a 3-1 aggregate victory in their semi-final tie, in the Clausura final over two legs next Thursday and Sunday.
Mexico will defend their title at the June 5-25 Gold Cup in the United States.
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