The Ivory Coast international was pelted with water bottles and cigarette lighters during the match, and it was suggested that the former Arsenal man had been a target of racial abuse from Besiktas' fans.
The Inonu Stadium outfit, however, stated that the fans' anger towards Eboue was caused by the Ivorian play-acting to mislead the referee.
"The treatment Emmanuel Eboue was given by Besiktas fans on Sunday has nothing to do with racism," said Besiktas spokesman Mete Duren.
"Similar treatment was given to a Turkish player during the game as well, the sole motivation for the act was Eboue's theatrics aimed at deceiving the referee."These are baseless allegations and should not be taken seriously, Besiktas fans have always had extra sympathy for African players because of the club's black-and-white colours.
"It's true that Turkish football has many issues to resolve, but racism is simply not one of them."
Besiktas are sixth in the Turkish League, with 18 points from 11 matches, while Galatasaray are third, with one point more.