Mourinho reportedly remarked that the Galatasaray bench was "jumping like monkeys" following an early challenge.
In response, Galatasaray announced plans to file criminal proceedings against Mourinho and lodge official complaints with UEFA and FIFA.
Fenerbahce issued a response, stating: "This statement has become necessary regarding a topic that has been on the agenda after the match played between our football team and Galatasaray.
"A statement made by Jose Mourinho after the match was taken completely out of context and deliberately distorted.
"As every common sense person can see and understand, these expressions, used by Jose Mourinho to describe the extreme reaction of the opposing team's technical staff to the referee's decisions during the match, can in no way be associated with racism.
"Trying to portray this discourse as racist is a completely malevolent approach. We would like to inform the public that we will exercise our legal rights regarding this pathetic slander that aims to take the competition out of the field, change the agenda and manipulate it."