The 33-year-old started his career with the Pittodrie outfit in 2000 before moving onto Plymouth Argyle eight years later.
He returned to the north east in 2011 but a knee injury sustained in pre-season has prevented him from featuring art all for Derek McInnes' side this season.
The Dons have now decided to release the player following 277 appearances and 13 goals for the club.
In a statement released on their official website, the club said: "Aberdeen Football Club has terminated the contract of Chris Clark. A long standing servant of the Club, Chris has fully recovered from the injury he sustained in a pre-season game in Ireland but has been unable to force his way into first team contention.
"Everyone at Pittodrie wishes Chris all the very best for the future."