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Moukoko, who became the youngest player in Champions League history last December, tore ligaments in his foot while on Germany Under-21 duty late last month.
He is sidelined for the European quarter-final, first leg in Manchester on Tuesday and the return on April 14, as well as the rest of Dortmund's Bundesliga campaign.
Moukoko sat out Saturday's 2-1 home defeat against Eintracht Frankfurt which left Dortmund seven points from the Champions League places with seven games left.
Moukoko became the youngest player in Bundesliga history when he made his debut the day after his 16th birthday last November.
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He also became the youngest goalscorer in Germany's top-flight when he netted in a defeat at Union Berlin on December 18 and has so far scored three goals in 14 league appearances.
ryj/pb