The 21 year old, a classic striker, netted twice in Monday's 6-0 thrashing of Norway, but Germany must wait until their next World Cup qualifier, against Northern Ireland in Belfast on October 5th, to secure their Russia 2018 place.
Werner came off to a standing ovation in Stuttgart, a far cry from the jeers and verbal abuse he suffered at the hands of German fans in Prague last Friday.
"That meant a lot to me, because this is my home town," said Stuttgart-born Werner after his double against Norway.
"I grew up here and I am pleased I could score twice to pay back the fans.
"Things were different, in terms of the emotion and attitude, compared to the Czech Republic match, we took it seriously from the first minute today.
"I believe we have got more used to the system, which the boys have been using for a while.
"Personally, I am delighted to have scored so often, it's been a lot of fun."
"I never thought it would turn out like this for me and I am so happy about it."
Werner has filled the void created when Germany's all-time top-scorer Miroslav Klose retired after the 2014 World Cup.
Klose, who now coaches Germany's strikers, netted 71 goals in 137 games to finally beat Gerd Mueller's phenomenal record of 68 goals in 62 matches for West Germany between 1966-1974.
Now Werner is walking in the footsteps of those legendary strikers, finally solving the issue Germany had 12 months ago when midfielder Mario Goetze played up front with limited success.
"Of course, we have too few options in this central position, which is a fundamental problem," a worried Thomas Mueller told German daily Bild a year ago.
Wish come true
"It would be conducive for German football if in the next few years players come along who are amongst the best in the world."
Yet nine months before the World Cup starts in Russia, Mueller's wish has come true.
It was the Bayern Munich forward who set up Werner for both of his goals on Monday.
A deft flick allowed Werner to tap home Germany's third before Mueller's pin-point cross was headed home just before the break.
Werner was the top German scorer in the Bundesliga last season with 21 goals in 31 games.
However, he has a bad reputation amongst German fans - branded a cheat after diving to earn a penalty in a German league win against Schalke 04, which has haunted him since December.
It was the reason why a group of German hooligans jeered him in Prague on Friday.
Germany's head coach Joachim Loew was unimpressed with the whistles and jeers Werner has endured for both club and country.
Beautiful side of football
"These insults against Timo are extremely painful. It's not fair and it's not funny. He made a mistake and recognized that," said Loew.
"I now call for the public to treat him like a full-time player of the national team."
Against Norway, Werner was applauded off on 66 minutes and replaced by veteran Mario Gomez.
The 32-year-old Gomez proved he will not yield his place without a fight by netting Germany's sixth goal on Monday and his 31st in 71 matches in the famous white shirt.
Gomez was full of praise for Werner: "He's a great lad and a great player.
I don't compare myself to him as we're different types of players".
Yet their is no doubt that Werner's all-action style suits the high-tempo game Loew wants better than the burly Gomez who has often only been a threat for Germany when in the box.
Loew was delighted with his team's performance in Stuttgart - and Werner's
"It was a great atmosphere and a lot of fun to play in Stuttgart, it showed the beautiful side of football," said Loew.
"It was the first home game here for a long time and you could see the fans were up for seeing their team, we also contributed our part to the mood with great combinations and goals."