Meier had been the Bundesliga's longest serving coach since Thomas Schaaf was sacked by Bremen but a 12-game winless streak at the end of the season cost him his job.
He had been at the club since 2008 and guided them up from Germany's third tier to the top division.
Club chairman Peter Frymuth said: "In view of the long time we have been working together successfully, we deliberately took our time intensely analysing the recent past.
"The facts which relegation has caused were only slightly determining and they were not the key.
"In consideration of many different factors, and after discussions with Norbert Meier himself, our collaboration will now be brought to a mutual conclusion."