The first came in the 25th minute when Luis Tejada, Panamaâ€™s leading scorer, was given a red card for deliberately and blatantly striking Francisco Rodriguez in the face on a high ball.
Panama players were outraged.
They furiously approached U.S. referee Mark Geiger face-to-face, laid hands on him and pushed him.
A scuffle including finger pointing, pushing and shoving endured between the two teams.
Despite playing out-manned, Panama was not deterred.
Roman Torres headed a goal on a corner kick from Erick Davis in the 57th minute to give Panama the lead.
The second controversial call occurred in the 88th minute when Panamaâ€™s team captain Torres fell on the ball inside his teamâ€™s penalty box and was called for a hand ball.
Following an eleven minute delay, which included more altercations between Panama and Mexico and fans throwing rubble onto the field, Mexico captain Andres Guardado scored on a penalty kick to tie the game.
In extra time Harold Cummings was given a yellow card for tripping Javier Hernandez.
11 total yellow cards were given out Wednesday night.
Guardado scored on another penalty kick to give his team the win.
Seconds after the final whistle Geiger was rushed upon by Panama players and had to be escorted off the field by security personnel.
Six time CONCACAF Gold Cup champions Mexico will take on Jamaica Sunday evening at Lincoln Financial Field in Philadelphia.