It was a well contested first 45 minutes at Signal Iduna Park, with the best chance falling to the hosts, but Youssoufa Moukoko directed his shot wide of the post from eight yards.
Pep Guardiola's men emerged from the interval with more attacking intent and just before the hour mark, Riyad Mahrez was fouled inside the box by Emre Can.
The Algerian stepped up for the spot kick, but saw his effort expertly saved by Gregor Kobel.
The goalkeeper was forced into action shortly after, denying Gundogan and Julian Alvarez in quick succession.
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Both sides couldn't find a way to get the ball in the net with the draw crowning City as Group G winners, whilst Dortmund also secured progression into the knockout stages with the point.
View the best images from the clash via our gallery below.