In a statement on Friday, Jennings thanked the Marlins and team owner Jeffrey Loria for what he called a "fun ride."
"After 13-plus years with the Marlins organization, I received a phone call yesterday from David Samson and Mike Hill informing me that I was being relieved from my position as general manager," Jennings said. "While this was certainly sad and regrettable news, I respect their prerogative to make changes and listen to new voices.
"It has been a fun ride during my time with the Marlins -- having the opportunity to serve as vice president of player personnel, general manager and field manager, and being part of the 2003 World Series championship. However, nothing is more special than the people. I would like to thank Mr. Loria and David Samson for employing me, and the wonderful Marlins office staff I was afforded the opportunity to work with, and most importantly, the Marlins players for their energy and effort and the opportunity to win their trust and respect this season."
The Marlins also announced on Thursday that Hill will assume all general manager duties.
Jennings, the club's general manager since Sept. 29, 2013, replaced Mike Redmond as manager on May 18. He inherited a 16-22 record, and with an injury-depleted roster, finished 71-91.
Under contract with the Marlins through 2018, Jennings said a few teams have already contacted him about potential positions.
"I wish the Marlins' players and the organization the best as we all move forward with our careers," Jennings said.
Joe Frisaro is a reporter for MLB.com. He writes a blog, called The Fish Pond. Follow him on Twitter @JoeFrisaro and listen to his podcast. This story was not subject to the approval of Major League Baseball or its clubs.