The Nigerian international scored the games opening goal in the 26th minute. Fenerbahce went on to win the game 2-1 with Fernando Belluschi and Bruno Alves scoring the games other two goals.
Fenerbahce will face Bursaspor in the second leg at the Sukru Saracoglu stadium on May 21.
The 28-year-old striker has fallen out of favour with Fenerbahçe fans and is expected to leave the club in the summer.
The Nigerian international was booed by his own fans in the recent Istanbul derby against Beşiktaş.
Emenike took off his shirt and walked off the field in protest but later returned to the game.
The powerful striker was given permission to go on leave after the incident but has since returned to Turkey.
Emenike has scored five goals in 32 appearances this season and has come under fire from sections of the press and fans.