Fortuna went down on the final day of the Bundesliga season after a 12-game winless streak saw them drop into the bottom two for the first time.
Meier, who was the Bundesliga's longest-serving coach following Thomas Schaaf's departure from Werder Bremen, has paid the price for the club's demise after just one season in the top flight.
"In view of the long time we have been working together successfully, we deliberately took our time intensely analysing the recent past," said club chairman Peter Frymuth.
"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."
Frymuth also hit out at the speculation in recent weeks which claimed Meier was going to be fired, even if they did not go down automatically.
"What we have had to experience in recent days was, in view of the serious work we always endeavour to deliver, downright unacceptable," said Frymuth.
"It seems like somebody has deliberately spread untruths and, by doing so, broken the rules of fairness.
"Somebody intentionally damaged the club, the people involved and also the coach. This can only be described with the word 'unbearable'."
Instead, Fortuna would prefer to look back on five and a half successful years with Meier at the helm.
"Norbert Meier led us on a successful path from the third division into the Bundesliga," said the club's long-serving director of sport Wolf Werner.
"Fortuna's promotions will permanently bear his name."