Van Persie scored with his first touch of the game after being brought on for Moussa Sow on 80 minutes.
The Dutch star scored a well timed header but the Greek side cried foul play claiming that a push was involved.
Van Persie denied claims that he pushed the Greek defender, instead stating that he used just used his strength.
“I used my body, as a striker you have to know how to use your body intelligently and that is what I did. The referee made the right decision,” Van Persie was quoted as saying by the Hurriyet after the game.
The 32-year-old scored his first goal for Fenerbahce since joining on a £4.7 million transfer fee from Manchester United last month.
Van Persie scored his first goal with his first shot on target since joining the Yellow Canaries.
The Netherlands international has yet to make a start for Fenerbahce but could be included in the starting XI against Rizespor on the weekend.