The team said Evans will be reassigned, with responsibilities to be determined.
The move came as the Giants began the final week of the season at 72-84, their second straight losing record.
"I made the decision, really," CEO Larry Baer said. "At this point, we needed to take a fresh approach to baseball operations."
The club will start a search for a new head of baseball operations.
"We're looking for someone that sort of is the 'next gen' general manager, if you will," Baer said.
"People will say 'new school versus old school,' people will say 'analytics versus scouting,' and I think that the new, next-generation general manager is able to do both, and will bring both to the mix."
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.
"He's a big part of our family tree," Sabean said. "I came into the organization in '93 and I believe Bobby shortly thereafter in '94. We've not only grown together in endeavors professionally with the Giants, we've grown together as people and it's a big part of your lifetime."
The Giants won World Series championships in 2010, 2012 and 2014. They made the playoffs again in 2016, but are 166-224 since taking a major league-best 57-33 record into the All-Star break that year.
Baer said the team is open to female candidates.
"Sure," he responded. "I haven't considered anybody yet, since we're just making this announcement now, but we would consider, of course, females."
Baer deflected the notion that the Giants were blaming Evans for their recent struggles.
"Brian Sabean and Bobby Evans at the helm over 26 years, I would match their record with pretty much anybody in the sport and even beyond the sport," Baer said. "So when we start talking about blame and start talking about that kind of thing, I mean I understand the question . you want to blame the last year and this year to some extent, but I don't step back and think of this in terms of blame, I think of this in terms of it's been an incredible run, an incredible journey, but it is time now to create the next - to create the blueprint of the future."
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