Werner, 38, joined RB Leipzig from Werder Bremen last summer, but despite taking them back to the Champions League, was sacked.
The German club have now confirmed that former Man City defender Martin Demichelis has now taken over.
Demichelis, 45, who was relegated from LaLiga with Mallorca last season, has signed a two-year deal with RB Leipzig.
Speaking to the club’s website, he said: “I was won over by my discussions with the club and its sporting vision. RB Leipzig are an ambitious club with a clear identity, outstanding talent and a determination to keep improving at the highest level. That is exactly the kind of challenge I was looking for.
“I have enormous respect for the work that has been done here. I want to build on those foundations and take the next steps together with the team.
“I want to create a side that plays bold, intense and exciting football, takes responsibility on the pitch and inspires the people of Leipzig with its passion.
“I’m also really looking forward to leading RB Leipzig in the Champions League. Testing ourselves against Europe’s best is an incredible challenge and exactly where a club with RB Leipzig’s ambition and quality belongs.
“I can’t wait to share those special nights with the team.”