After ongoing discussions with their management, the pair had each agreed to play their final game in the red, white and black in round 23 against Adelaide.
Senior coach Alan Richardson thanked them for their service to the club.
“James and Clint have played a significant role in a highly successful era in the football club’s history and both been fantastic servants of this club over many years. The way they carried themselves today is a testament to their professionalism and class,” he said.
“After honest conversations with James and Clint over the past few weeks, they understand the direction the club is taking through this rebuilding phase.”
Gwilt played 126 games for the club after debuting late in 2005, while Jones notched 149 matches with St Kilda after he was recruited from South Fremantle in the 2006 AFL Rookie Draft
Gwilt has indicated he would like to explore other options after ten years at the club, while Jones is yet to make a decision about his playing future.
