The win sets up a clash with Paris St. Germain on December 19 to decide who progresses through as the Group winner.
The Italians started brightly, using the width of the pitch to stretch Fenerbahce and were rewarded for their efforts after 24 minutes when Matteo Gerbaudo calmly slotted past the keeper.
The remainder of the first half ebbed and flowed without many chances for either team and at the break the score was 1-0.
The Turks had mixed fortunes at the start of the second half with a red card for their left-back Taskin, before Cici grabbed an equalising goal just minutes later.
The Italians regained their composure and were dominant with possession, and found a late winner through Schiavone to take the three points.
Fenerbahce finish bottom of Group 2 without a win in the competition.