Ersun Yanal's side went into their home clash with the reigning champions having seen their advantage at the summit reduced to one point after second-placed Kasimpasa defeated Gaziantepspor 3-0 on Saturday.
However, Fenerbahce reclaimed their leading margin with a hard-fought victory over Roberto Mancini's Galatasaray.
Midfielder Emre Belozoglu opened the scoring at the Sukru Saracoglu with a 24th-minute penalty before Cristian Baroni sealed the win with a strike midway through the second half.
Felipe Melo had the chance to pull one back for the visitors from the spot in injury time, but his tame effort was saved by Volkan Demirel as Fenerbahce extended their unbeaten league run to 10 matches.
Kasimpasa kept the pressure on Fenerbahce at the top thanks to a three-goal blitz in nine first-half minutes against Gaziantepspor, with Ezequiel Scarione, Castro and Ilhan Ekher on the scoresheet.
Third-placed Sivasspor, meanwhile, made it six wins in their last seven Super Lig games with a 2-1 home success over Bursaspor on Saturday, with second-half goals from Burhan Eser and Aatif Chahechouhe sandwiching a Taye Taiwo equaliser.
At the other end of the table, bottom-placed Kayserispor were condemned to their seventh defeat in 11 games as Besiktas ran out 3-0 victors at the Kadir Has Sehir Stadi on Saturday.
Meanwhile, second-bottom Elazigspor fell to their seventh defeat in a row with a 1-0 reverse to Kayseri Erciyesspor, but Konyaspor put breathing space between themselves and the relegation zone with a 2-0 success over mid-table Antalyaspor.
Eskisehirspor moved above Galatasaray into fifth thanks to their 2-0 win against Akhisar Belediyespor on Friday, with second-half goals from Hurriyet Gucer and Necati Ates enough for the hosts.
Elsewhere this weekend, Genclerbirligi came from two down at home to Trabzonspor to make it three Super Lig wins in a row with a 3-2 success, while Karabukspor beat Rizespor 2-1.
