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Dortmund has failed to score for the first time since September 2020.
After playing 50 minutes with 10 players, Borussia Dortmund fell to fourth place in the Bundesliga.
Marco Rose's disappointing return to his old club was ended by Denis Zakaria scoring the only goal.
After a rebound from Jude Bellingham, the Switzerland midfielder did a one-two match with Matthias Ginter and then fired past Gregor Kobel.
Three minutes later Mahmoud Dhahoud was sent for a second yellow.
Dortmund played without Erling Braut Hailand, the injured forward, and Marco Reus as club captain. Dortmund struggled to get in front of goal and couldn't score a single goal.
Their best chance came at injury time, when Belgium's winger Thorgan Hazard was sent over.
This means that Dortmund's streak of scoring consecutively in all competitions is over at 56. It began with a 2-0 loss at Augsburg 26 September 2020.
Bayern Munich will be three points clear of Wolfsburg at the top Bundesliga table after it also lost 3-1 to Hoffenheim.