Volkan Sen opened the scoring in the third minute when he met Caner Erkin’s set-piece delivery on the volley smashing the ball into the bottom corner giving keeper Besiktas keeper Tolga Zengin no chance.
The Yellow Canaries ended the first half in the lead but suffered a few nervy moments in the second half.
Marcelo looked to have equalised with a header that left Fenerbahce keeper Volkan Demirel stranded but his effort hit the post – seventh time in six games the Black Eagles have struck the post.
Besiktas had a few more chances to equalise but it was second half substitutes Ozan Tufan and Luis Nani who combinated for the second goal.
Tufan burst into the box and setup the Portuguese international for one of the easiet goals he has ever had to score on 83 minutes.
Nani has now scored nine times for Fenerbahce since joining from Manchester United with eight being converted at home.
The Portuguese international scored his first home goal since leaving the Premier League giants over the summer.
Fellow ex United star Robin van Persie also started but was unable to find the back of the net.
Fenerbahce have lost just once in the league at home over the last three seasons and moved two points clear of Besiktas at the top of the table following the victory.
Stadium: Sukru Saracoglu
Referee: Cüneyt Çakır
Kick-Off: 18:00 GMT
Fenerbahce: Volkan, Gökhan, Alves, Kjaer, Caner, Josef, Mehmet Topal, Diego, Alper Potuk, Volkan Şen, van Persie
Manager: Vitor Pereira
Besiktas: Tolga, Beck, Alexis, Marcelo, İsmail, Atiba, Oğuzhan, Sosa, Quaresma, Olcay, Gomez
Subs: Boyko, Töre, Tosic, Kurtuluş, Arslan, Uysal, Tosun
Manager: Şenol Güneş
Goals: 3′ Volkan Sen, 83′ Luis Nani