The former Netherlands forward struck in both halves on Saturday and Caner Erkin added a third goal in stoppage time for the in-form leaders.
Istanbul giants Fenerbahce are now unbeaten in nine matches, with eight of those ending in victory for the champions.
Besiktas responded to a home defeat against Galatasaray in their last Super Lig encounter by beating Genclerbirligi 2- 0 on Monday.
Demba Ba opened the scoring in the second half with his 18th goal of the season and Olcay Sahan sealed the points for Slaven Bilic's side.
The game ended on a sour note for Besiktas, though, as Pedro Franco was shown a straight red card for upending Berat Tosun.
Galatasaray put their shock Turkish Cup defeat to Diyarbakır Buyuksehir Belediyespor behind them by seeing off struggling Rizespor 2-0 on Sunday.
Wesley Sneijder and Bruma did the damage for Hamza Hamzaoglu's men, who were humiliated in a 2-0 midweek cup defeat against 2. Lig side Diyarbakır at the Turk Telekom Arena.
Bursaspor moved up to fourth spot courtesy of their 3-2 win at Konyaspor, which was sealed courtesy of Fernandao's stoppage-time strike, and Istanbul Basaksehir's 2-2 draw with Mersin Idmanyurdu.
Balikesirspor remain bottom of the table after they were beaten 1-0 at Gaziantepspor on Saturday, while Sivasspor's four-game unbeaten run ended with a 3-1 defeat at Trabzonspor - Oscar Cardozo scoring twice.
An entertaining contest between Akhisar Belediyespor and Eskisehirspor finished 2-2 on Saturday, while Kayseri Erciyesspor moved up to 12th with a 2-1 win at Karabukspor on Sunday.
