San Francisco said Monday that Evans will be reassigned, with responsibilities to be determined.
The Giants began the final week of the season 72-84, their second straight losing record.
The team will start a search for a new head of baseball operations.
Evans was hired by the Giants in 1994, became vice president of baseball operations in 2009 under general manager Brian Sabean and was promoted to GM in April 2015 when Sabean became executive vice president of baseball operations.
A major league-best 57-33 at the 2016 All-Star break, the Giants are 166-224 since.
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