The 21-year-old was making his senior international debut at SIGNAL IDUNA PARK, but had to be replaced by Bayern Munich's Thomas Müller in the 77th minute as Die Mannschaft secured a 1-0 win over England.
Germany coach Joachim Löw praised Werner for what he termed "an insane amount of running" during the game, but Leipzig's rising star appears to have paid the price for his high-intensity performance after suffering a hamstring tear in his left thigh.
The injury means Werner will play no part in Germany's World Cup qualifier in Azerbaijan on Sunday, where they will be looking to maintain their perfect start in Group C with a fifth win in five games.
"It was a great first game and I really enjoyed it," said Werner, who left the team base in Kamen for Leipzig on Thursday. "Hopefully I will be able to come back a few more times yet."
Currently RB's top scorer with 14 goals in the Bundesliga, Werner is also likely to miss his side's Matchday 26 clash at home to Darmstadt on Saturday 1 April.