Gordon Strachan's team begin their bid to reach a first major finals in 18 years on 7 September at the 65,718-capacity Westfalenstadion.
Scotland's last visit to Germany was a 2-1 defeat in Dortmund in 2003.
Scottish Football Association chief executive Stewart Regan confirmed the venue on Twitter, saying: "The German FA have now confirmed that Scotland will play Germany on 7th Sept in Dortmund. Get your flights sorted quickly! #comeonscotland."
Scotland will also take on Georgia, Poland, the Republic of Ireland and Gibraltar in Group D as they aim to reach the next European Championship finals in France.
When the draw was made last month, Strachan said: "The Germans might make one mistake, possibly two, but I don't think they have failed to qualify for a major tournament, so the rest of us will be looking for second place.
"It will be really tough for everyone in the group."