Fenerbahce found an early goal from Mert Hakan Yandas in the eighth minute at Bosuilstadion in Antwerp, Belgium.
The second goal came from Max Meyer in the 16th minute while Mergim Berisha produced his team's third goal in the 29th minute.
In another Group D match, Eintracht Frankfurt claimed a 2-1 away victory over Olympiacos at Stadio Georgios Karaiskakis in Piraeus.
Eintracht Frankfurt are currently at the top of the group with 10 points. Second-place Olympiacos collected six points, while third-place Fenerbahce have collected five points from four matches.
Antwerp are at the bottom of the group with one point.
