Reports said that Click turned down a one-year contract from the Astros, which led to him and the team deciding to part ways.
In a statement, Crane thanked Click for helping build the Astros to become the winningest team in the American League with 108 wins and a World Series title.
“We are grateful for all of James’ contributions,” Crane said. “We have had great success in each of his three seasons, and James has been an important part of that success. I want to personally thank him and wish him and his family well moving forward.”
Click was brought to Houston from Tampa Bay in 2020 after the Astros fired Jeff Luhnow and manager A.J. Hinch for their role in the sign stealing scandal in 2017 and 2018.
Under Click, the Astros have won two AL West Division titles in 2021 and 2022 and reached the AL Championship Series for all three years, winning two pennants.
Despite leading the Astros to an AL pennant in 2021 and a World Series title in 2022, Click was working without a contract as of Oct. 31, and was in Las Vegas while Crane announced a new one-year deal for manager Dusty Baker for 2023.
It’s believed to be the first change in general manager following a World Series title since 1947, when the Yankees’ Larry MacPhail was replaced by George Weiss.
The Associated Press contributed to this report.