Moussa Sow’s 65th second goal was the opener as Jose Mourinho’s side traveled to Turkey on Thursday night.
The visitors dominated possession but saw world record signing Paul Pogba go off with a leg injury in the first half.
Jeremain Lens also curled in a brilliant free-kick in the second half as the Red Devils struggled harder to get a goal.
Their effort later turned to celebration as Wayne Rooney smashed in a 25-yard consolation goal in less than two minutes to the end of the game.
Manchester United are now third in Group A with one point behind leaders Feyenoord and Fenerbahce.
They have two games left against the Dutch side at Old Trafford and away to Ukraine’s Zorya Luhansk.