Rooney has shaken off a thigh problem to replace out-of-form Ibrahimovic at the tip of the Man United attack, while Frenchman Anthony Martial has also returned from injury to start in a wide position.
As for Fenerbahce, former Man United striker Robin van Persie is only named on the bench.
Emmanuel Emenike impressed after coming off the bench in the reverse match last month, but the centre-forward's position goes to Moussa Sow, while fit-again Jeremain Lens, formerly of Sunderland, also returns to the home side's XI.
Fenerbahce: Volkan; Sener, Kjaer, Skrtel, Ali; Mehmet, Josef, Alper; Lens, Sow, Sen
Subs: Fabiano, Van Persie, Koybasi, Emenike, Neustadter, Salih Ucan, Stoch
Manchester United: De Gea; Darmian, Blind, Rojo, Shaw; Schneiderlin, Herrera; Rashford, Pogba, Martial; Rooney
Subs: Romero, Jones, Fellaini, Mata, Mkhitaryan, Young, Ibrahimovic
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