Bruins GM Peter Chiarelli confirmed the breakup at the team's end-of-season press conference Wednesday at TD Garden.
Jagr also spoke to reporters about his time in Boston and joked "Maybe if I scored 20 goals in the playoffs it would be a different story, but I was 20 short."
The future Hall-of-Famer did say he hopes to join another NHL team next season.
"I want to do it [play in the NHL again], I love this game so much that's for sure," Jagr said. "So I don't want to go back to Czech yet."
Jagr played 33 games with the Bruins and would end his time in Boston with just two goals and 17 assists on the offensive side, although he made contributions in other areas of the game.
“I told him that ‘what you did to wear a D down was very impressive," Chiarelli said. "I know you didn’t score, but the timely plays that you made were terrific. I thought you spread out our play, which helped our power play'. I was really happy with Jaromir.”
Jagr also revealed to reporters that he hurt his back and hip in Game 6 of the Stanley Cup Finals vs. the Chicago Blackhawks.
"It was something wrong with my back and my hip so I had a tough time to skate," Jagr said. "But I talked to the doctor they gave me some shot but it took like 30 minutes to knock the pain off so I couldn't really play in the second period."
Chiarelli also said the Bruins won’t be re-signing defenseman Andrew Ference or local product Jay Pandolfo.
"With the current cap Peter [Chiarelli] isn’t going to be able to keep me," Ference said. "So you know, he’s got to resign Tuukka [Rask], and obviously do his side of the business. Also unfortunately with the new CBA he’s restricted. He said ‘wish it wasn’t so,’ but that’s the way it is."
Bruins forward Nathan Horton could also be taking his services elsewhere next season. He was asked what his priorities were when looking at his next contract.
"I’m not even going to talk about it," Horton said. "If you want to talk about it you can call my agent. We just play hockey and that’s all we worry about. Sooner or later, like I said, it’s going to get taken care of and we’ll all find out what it’s going to be. I don’t know either, so I can’t tell you. And that’s it."
Horton will require surgery on his dislocated left shoulder. Horton said the shoulder popped out in overtime of Game 1 against the Blackhawks. Horton played with a brace for the rest of the series.
Chiarelli told Horton that the Bruins hope to re-sign him and said that he will not be using amnesty buyouts.