The team announced Monday that Evans was being removed from the job and will be given a different role.
"I want to thank Bobby for his tireless work on behalf of the Giants," team president and CEO Larry Baer said in a statement. "He played an important role in our team's success throughout his tenure, which includes three World Series championships, four NL pennants, and eight playoff appearances. We look forward to new leadership to continue our historical record of success."
Evans joined the team's front office in 1994 and was an assistant general manager for nine seasons before becoming the GM.
Sabean said in a statement Monday, "I take great pride in the longstanding continuity of our baseball department. I want to express my thanks to Bobby for all he has given to the Giants over the past 25 years and for his countless contributions. I'll be working closely with Larry as the organization finds its next leader of baseball operations."
Many of Evans' major deals have been busts.
He gave right-hander Johnny Cueto a six-year, $130 million free agent contract in December 2015. Cueto went 18-5 with a 2.79 ERA in 2016 but has combined for just 11 wins over injury-plagued seasons the past two years.
The same month that Cueto signed, right-hander Jeff Samardzija got a five-year, $90 million deal. Samardzija is 22-31 as a Giant, and he missed the second half of this season due to a right shoulder injury.
Perhaps most glaringly, Evans signed right-hander Mark Melancon for four years and $62 million in December 2016 to be the Giants' closer. Melancon lost his ninth-inning role last year and hasn't regained it. He is 14-for-23 in save chances for San Francisco to go with a 1-5 record and a 3.82 ERA.