Joachim Low's Germany have now gone over seven games without conceded a single goal, having beaten England 1-0 in Dortmund on Wednesday.
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Gareth Southgate took charge for the first time following his official oppointment as Three Lions boss, but his side were unable to break down a stringent Germany backline.
Lukas Podolski, marking his final game in international football, struck a second-half winner to secure a narrow 1-0 lead in the Friendly at Signal Iduna Park.
It also marked the eighth consecutive fixture in which England failed to keep a clean sheet against Germany, and their third defeat in four meetings between the two sides.
Former Arsenal man Podolski won his 130th cap for his country and bowed out with a spectactular strike from distance - his 49th of his international career - before leaving the pitch on 83 minutes to a standing ovation.
Before the game, Podolski told fans: "I want to personally say thank you for 13 awesome years on & off the pitch. You fans have played a big part in that."