The Allianz Arena was treated to a goal-fest on Tuesday as the home side stormed to victory to establish a four-point lead at the top of the Bundesliga standings.
Jamal Musiala opened the scoring for the Bavarians in the sixth minute. Anthony Jung gave Werder a glimmer of hope when he equalised four minutes later.
However, Serge Gnabry netted a hat-trick, while Leon Goretzka and Mathys Tel also found the back of the visitors' net to secure a one-sided victory.
Werner admitted after the game that he was "annoyed" with the 6-1 result.
"Bayern Munich showed today that they are in a different league - at least in their current form," said Werner, as per the official Werder Bremen website.
"We got off to a reasonable start in the game. We won a lot of high balls, but unfortunately, we weren't really able to switch the play.
"Every mistake we made was punished by Bayern. We lost the game in that period from the 20th to the 30th minute. In the second half, Bayern took their foot off the gas.
"We could have gone home feeling different at 4-1 but at 6-1 that annoys me. Still, I have to say that we're not the first side to be on the end of a result like that here."