On Thursday, Trabzonspor filed a civil law suit at an Istanbul court accusing Emre, as he is popularly known, of abusing Zokora.
The accusation, denied by Emre, cast another cloud over 2011 league champions Fenerbahce whose chairman is currently on trial as a suspect in a multi-million dollar match-fixing scandal that rocked Turkish football last year.
Zokora first levelled the accusation against Emre at a news conference following Fenerbahce's 2-0 home win in Istanbul over Trabzonspor.
"Emre and I had an argument during the game. I beg your pardon for saying this, but he insulted me by saying nigger. What upsets me more is how disgraceful it is for a player who has African team mates like Sow and Yobo to insult an African from another team," Zokora said.
The following day, Emre told a news conference that he had abused Zokora verbally in English without using racist terms, and that such abuse was commonplace during matches.
"If I have even a little bit of racism, may God take my heart away from this body," Emre said.
The Turkish Football Federation (TFF) subsequently referred the matter to the disciplinary committee, which decided on the ban.
"Due to the insult to the player of the rival team, it has been decided with the majority of votes to punish Fenerbahce player Emre Belozoglu by sanctioning a ban for two official games," the PFDK said on its website.
Had the committee decided the abuse was racial, Emre could have received a lengthier ban of four to eight matches.
The teams are playing in the playoffs against Galatasaray and Besiktas for the domestic championship. Trabzonspor were runners-up to Fenerbahce last year, but took Fener's place in the Champions League due to the match-fixing probe.