The Germany Under-19 international has established himself in the starting XI at the Mercedes-Benz Arena this season and celebrated his 18th birthday by penning a new deal with Thomas Schneider's side.
Stuttgart are only above the relegation zone on goal difference following a dismal run of eight consecutive Bundesliga defeats.
But that streak has not undermined Werner's passion for his boyhood club, with the teenager quick to express his delight after signing the deal.
"VFB (Stuttgart) is my club and has been since I was a little boy – which is why I am so happy about this contract," Werner told the club's official website.
"I went through all of VfB's youth teams and feel completely at home here. I want to continue learning and I am delighted to be able to do just that at my club."
Werner has scored four goals in 25 appearances for Stuttgart this season, and director of sport Fredi Bobic is confident that he can continue to develop with the five-time German champions.
"It was always our plan to carefully build up Timo and give him time to develop," Bobic said.
"He has exceptional assets and possesses the great strengths of speed and an instinct for goals.
"Timo is a young professional and is doing very well in his first Bundesliga year. We want to provide him with the best possible support along his way and we firmly believe that we will have many years of enjoyment with him in the team."
