Willi Orban's 98th minute strike three minutes past the official time added secured RB Leipzig's win to knock Borussia Dortmund out of the German Cup.
Former Chelsea player Timo Werner opened the scoring the 23rd minute and although Dortmund looked to control much of the second half, they couldn't find a response.
Jude Bellingham started on the bench and was introduced in the 63rd minute, but couldn't help his side climb back into the match.
Dortmund's exit from the competition will leave a Bundesliga title win their last shot at silverware this season.