The Super Eagles striker was facing his former employers for the first time since he left them to join Spartak Moscow in July last year.
Emenike opened scoring in the 59th minute, after latching onto a cross from Dmitry Kombarov. But Fenerbache got a crucial away goal when former Liverpool striker Dirk Kuyt levelled the scores six minutes later.
The Russians however regained their lead when Dmitry Kombarov smashed in Aiden McGeady's corner four minutes later, to hand Spartak Moscow a narrow win going into the second leg which is billed to be played on the 29th of August.
Emenike left Fenerbache in controversial circumstance, after he was implicated in a match fixing scandal which saw him spend a short time in an Istanbul jail, and had Fenerbache president Aziz Yildirim sentenced to six years imprisonment.
He has however found a home in Moscow, having settled in at Spartak, for whom he scored 14 goals last season in the Russian Premier League, to finish as the third highest goal scorer, behind CSKA Moscow's Seydou Doumbia and Zenit's Aleksandr Kerzhakov.
Fenerbache currently have Super Eagles captain Joseph Yobo on their payroll, and he was on for the entire duration of the game. While Emenike was substituted in the 72nd minute.