The encounter between two teams fighting alongside fellow Istanbul club Galatasaray for the Turkish Super Lig saw several flash points - particularly in a hotly contested first half at the Sukru Saracoglu Stadium.
One such incident involved Fener striker Emenike, the Nigeria international having earlier missed a sitter when one-on-one with Volkan Demirel, who took off his shirt and headed towards the tunnel.
Team-mates convinced him to return, but unsavoury scenes followed when both sets of players came together following a heated exchange between Fener captain Emre Belozoglu and Beskitas coach Slaven Bilic.
Emenike was eventually substituted in place of Pierre Webo at half-time, and it appeared as though the teams would play out a goalless draw until Moussa Sow volleyed home a fine 91st-minute winner.
Galatasaray beat Kasimpasa 3-2 to knock Besiktas off top spot, with Fener just two points off the pace to ensure a tense title race is to come.
Hamza Hamzaoglu's side were made to work for their victory, coming from two goals down to beat Kasimpasa 3-2.
Shota Arveladze resigned as Kasimpasa head coach last weekend having ordered his team to concede in the 2-1 loss to Konyaspor, as they took the lead when opposition player Ryan Babel was laid on the turf injured.
Jan Wouters has taken temporary charge and goals from Andre Castro and Tunay Torun put them in a surprise 2-0 lead by half-time at the Recep Tayyip Erdogan Stadium.
However, Gala roared back with a three-goal 13-minute blitz after the break, with Selcuk Inan, Umut Bulut and Burak Yilmaz all on the scoresheet.
Also on Saturday, Batuhan Karadeniz scored twice as Sivasspor eased their relegation fears in a 4-1 rout of UEFA Europa League hopefuls Bursaspor, Gaziantepspor won 1-0 at Mersin Idmanyurdu and Rizespor bested Kayseri Erciyesspor 3-0.
Sunday saw Doka Madureira score twice as Istanbul Basaksehir netted three times in the final six minutes to defeat Genclerbirligi 3-1, while Trabzonspor saw off Akhisar Belediyespor 2-0.
The weekend's action started with bottom club Balikesirspor picking up a crucial 4-1 victory at home to Eskisehirspor on Friday, with Isaac Promise and Ronald Vargas both scoring twice in a four-goal first-half blitz, while Konyaspor were 1-0 victors at Karabukspor.
