The Panama players were incensed by a last-minute penalty awarded to Mexico, which led to a late equaliser, before Mexico won 2-1 in extra time in Atlanta on Thursday thanks to another penalty.
"We met with both the referee department leadership and referee Mark Geiger," CONCACAF President Alfredo Hawit said in a statement on Saturday.
"We at CONCACAF regret these circumstances but accept that such human errors are part of the game."
Late Morris goal seals USA sixth Gold Cup
Panama claimed that American referee Geiger acted with the "clear intention of harming our eleven" in the match against Mexico, and that it was the "last straw" of a string of bad decisions throughout the tournament.
Costa Rica, which also lost to a late penalty by Mexico in the quarter-finals, said their team had been "directly affected by the poor work of the officials".
Panamanian goalkeeper Jaime Penedo and fellow player Luis Tejada were suspended for two matches and the nation's federation fined by the CONCACAF Gold Cup disciplinary committee on Friday following that semi-final defeat.
Penedo was punished for pushing an assistant referee after the controversial loss, while Tejada drew a one-match ban for the red card he received in the semi-final and an additional match for failing to leave the field in a timely manner.
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Jamaica and Costa Rica advance in Gold Cup