Both sides were edgy in the opening stages but as the visitors started to come into the game, they came close through Damir Vrancic, who shot wide from just outside the box.
It got worse on the half-hour mark for the away side, as Andre Hahn was allowed too much space in the box to direct a low shot beyond Daniel Davari.
Then three minutes later the contest was as good as over. Werner broke and found Hahn through the middle, who slotted in for 3-0.
Immediately after the half-time break Braunschweig had one back as Torsten Oehrl fired low from outside the box into the bottom corner.
However, any hopes of a comeback disappeared as Halil Altintop thrashed a left-footed effort high into the net from an angle.