Jamie Mata scored the decisive goal for the visitors five minutes after the break after he was set up by Brazilian winger Kennedy.
Trabzonspor are rooted to bottom spot in the Group C with one point from five games.
In another early kick-off game, Manchester United’s youngsters were dealt a harsh footballing lesson as Astana came from behind to condemn the Red Devils to a 2-1 defeat in Kazakhstan.
With their passage to the knockout phase already secure, ole Gunnar Solskjaer handed seven players – of which six where teenagers – their full club debuts in the Group L clash in what was the youngest-ever side Manchester United had fielded in European competition.
Solskjaer’s faith was repaid inside 10 minutes when captain Jesse Lingard drilled United into a deserved lead.
The youthful United side enjoyed a measure of control throughout but their failure to convert their dominance came back to haunt them as Dmitry Shomko hauled Astana level on 55 minutes, 38 seconds after Tahith Chong spurned a glorious chance to double the visitors’ lead.
Debutant Di’Shon Bernard’s unfortunate own goal seven minutes later then sealed Astana’s first Europa League points of the season and their first win over English opposition as United tasted defeat in Europe for the first time this campaign.
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