The former Tottenham Hotspur man has called for further punishment for the Turkey international, who admitted the remarks, but said they were made in the heat of the moment
The hosts prevailed 2-0 in a hotly-contested match, and in the wake of the game, the former Tottenham midfielder claimed the 31-year-old aimed a racial slur in his direction.
"Emre and I came face to face during the match. I'll tell you what he said word for word. He called me: 'A f*cking n*****'," Zokora told Lig TV after the match.
"This is the first time in my life something like this has happened to me. Emre has Africans like [Joseph] Yobo and [Moussa] Sow as team-mates - I can't understand why he'd say such a thing.
"We're trying to get on with our jobs. What does the colour of our skin matter? Fans, Fifa, the press are all against racist statements.
"I hope something like this doesn't go unpunished."
Emre was also accused of racially abusing erstwhile Everton duo Joleon Lescott and Tim Howard during his time at Newcastle but was quick to deny the allegations.
However, on this occasion, he has admitted that he spoke out of turn, attributing the remarks to on-pitch rivalry, claiming the matter was soon forgotten by both parties.
"In the heat of the moment in matches, you say bad things to one another. I used a stupid word, but he was also insulting me," he protested.
"We apologised to one another five minutes later, and hugged after the match. I'd like to apologise to everyone I know. For my part, I'd like to apologise for everything I said."
Fenerbahce's victory over Trabzonspor has closed the gap with Galatasaray at the top of the Super Lig championship play-off group to just two points.