The Phillies scheduled a press conference to announce the news, in which Manuel was replaced by third-base coach Ryne Sandberg.
"I did not resign and I did not quit," Manuel said. "I think it was an agreement."
Since the All-Star break, the Phillies have gone 5-20 and are on their way to having their first losing season since 2000.
Manuel has put up a record of 780-636 since replacing Larry Bowa in 2004. He was the longest-tenured manager in the National League and third-longest in Major League Baseball.
"Do I like the decision? No," Manuel said. "But they are doing the best thing they think is right for this team.
"I can't explain to you guys what the last nine years have meant to me. I have had some of the best times of my life here. Philadelphia has been the highlight of my career."