Gordon Strachan’s side went into the interval level after coming from behind twice with Mats Hummels’ own-goal and a James McArthur strike cancelling out a Thomas Muller double.
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But Ilkay Gundogan’s 54th-minute goal proved to be the winner for the world champions and, with two pool fixtures left for the Scots – at home against second-placed Poland and away to minnows Gibraltar – they remain in fourth place.
Scotland are now left vying for the play-off spot in the group – most likely with the Republic of Ireland – as they cannot finish in the top two automatic qualifying places.
The Germans are top with 19 points and a draw against the Irish on October 8 would be enough to secure their place in the finals.