The pair clashed during last Sunday's Super Lig game in Istanbul and the Ivorian subsequently accused the Turkey international of racially abusing him
Former Ivory Coast international Zokora had accused Emre of racially abusing him during last weekend's Super Lig clash between their respective clubs.
However, while Emre has been deemed guilty of insulting the former Tottenham Hotspur man, he has not been found to have used a racial slur.
Trabzonspor president Sadri Sener was quick to express his disgust with the ruling and attacked the character of Emre, with whom he claims to have had a run-in following Turkey's Euro 2012 qualifier against Belgium in June of last year.
"Racism is a horrible crime," he told Trt. "They should have ended his football career, but he has been banned for two matches!
"After we [Turkey] played away against Belgium, Emre was waiting at the gate of the airplane to beat me. There are witnesses.
"That day, they told me he'd 'never wear his nation's jersey again'. The situation is clear: Emre is this kind of man."
Emre was charged with using racially-aggravated language by the Football Association during his time with Newcastle United.