The midfielder has agreed a new deal which will keep him with the Bundesliga side until 2017.
The 28-year-old told kicker-Sportsmagazin: "I have never denied I am very much delighted to be at FC Augsburg. Me and my family like being around here. We have all made great sporting progress through the years I have been with FC Augsburg."
General manager Stefan Reuter added: "Tobias Werner is a fundamental part of our first-team squad. He has been with the club all the way through those recent five great years and he is full behind the club, the city and the Augsburg region as well. We are happy he stays on."
Augsburg currently sit 12th in the Bundesliga table.