The 33-year-old was filmed throwing his jersey on the ground after he was replaced with Umut Nayir in the second half.
He later rendered an apology to the club but explained that his actions were misinterpreted.
Without the former AC Milan ace, the Black Eagles managed to thump Denizlispor 5-1 to move up to 5th on the table.
After the match, he took to Twitter to congratulate his teammates for a wonderful performance.
He is expected to return to the squad for the match against Konyaspor on Friday.
Boateng has scored two goals in seven matches for the club since joining in January from Fiorentina.
Read Full StoryWell done eagles, great win! Let’s keep going on this way ???????? ???? #DENvBJK @Besiktas #Deligibiseverim pic.twitter.com/g8guGENH4a
— Kevin-Prince Boateng (@KPBofficial) June 20, 2020

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