The 21-year-old Werner had to be taken off in the 77th minute of their 1-0 friendly win over England in Dortmund and further checks showed he had torn muscle fibre in his left thigh.
It was not yet clear how long the RB Leipzig forward, who has scored 14 times in the Bundesliga this season to keep his club in second place, would be out of action.
Germany will have several players back against Azerbaijan, including striker Mario Gomez, who did not play against England due to a minor injury.
The world champions are five points clear at the top of Group C, having won all four matches so far.
(Reporting by Karolos Grohmann; Editing by Toby Davis)
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