The hosts took the lead on the half-hour mark when Matthias Ginter sent a lofted cross into the box, where Shinji Kagawa rose high to head the ball into the left side of the goal and beyond Ralf Fahrmann.
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Dortmund, however, ended the half in front after Matthias Ginter outjumped the opposition defenders inside the six-yard box to meet a corner with a thumping header past Fahrmann.
Three minutes after the restart Thomas Tuchel's charges extended their lead when Gonzalo Castro sent a pass to Pierre-Emerick Aubameyang, who showed good composure inside the box to bury the ball into the bottom-right corner.
The visitors managed to peg their opponents back to within a goal in the 71st minute when Huntelaar collected a pass and, from inside the box, lifted the ball over Roman Burki, who was off his line.
Nevertheless Andre Breitenreiter's side could not find another equaliser as their opponents saw the game out and clinched all three points.