Dortmund opened the scoring when debutant Marco Reus struck early on.
Theodor Gebre Selassie levelled with 15 minutes left for Werder, but just over five minutes later Goetze pounced to steal the points for the champions.
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Chelsea have struggled to build momentum in the opening stages of the campaign and are currently looking over their shoulders at the relegation zone.
Who of Europe’s top strikers will move to England this summer?