The referee was forced to halt proceedings in Trabzon after 55 minutes as a result of home supporters pelting the Ersun Yanal's players and staff with a number of missiles
The Istanbul club were leading the match 1-0 thanks to Emmanuel Emenike's first-half strike but the home supporters soon began pelting the Super Lig leaders with a variety of missiles.
The game was initally stopped after 28 minutes, forcing a total of 10 minutes added time to be played before the referee finally decided to abandon the match.
Fener players and staff were the primary targets of the violence, with pictures showing burnt holes in the shirt of goalkeeper Volkan Demirel.
The game is expected to be awarded in Fenerbahce's favour but no official announcement has been made as of yet.
The two clubs' fierce rivalry stems back to the 2010-11 Super Lig title race, when Fener produced an extraordinary run of results to pip the Black Sea side to top spot on goal difference.
Their title triumph was subsequently investigated in a lengthy match-fixing case, which saw Fener president Aziz Yildirim given a prison term.