The 66-year-old Magowan will retire from his duties at the end of the season on Oct. 1 but maintain an ownership stake, the team said Friday.
"I feel happy, I feel relieved, in some ways I feel a little bit nostalgic," Magowan said. "The memories I have are some very, very good memories and some memories not so good."
American Bar Association president and longtime Microsoft attorney Bill Neukom, a current partner in the Giants group, will take over for Magowan. Also, executive vice president Larry Baer will become team president effective Oct. 1.
These changes are subject to the approval of Major League Baseball. The Giants expect that to happen when the owners next meet, Aug. 13-14 in Washington.
"I couldn't resist it," Neukom said of the opportunity. "I couldn't have done this a year ago."
Magowan informed the ownership group of his decision during a meeting Friday morning. He plans to spend more time with his family once he's through, including seeing more of his 10 grandchildren.
"I'm sure there are a lot of you who will say there have to be other reasons," he said. "'You're fed up with last place or the Bonds investigations or the Mitchell Report or Bud Selig or whatever. And I'm going to tell you whether you believe it or not, it's the truth for me, that's not right. I'm leaving because I think the time is right for me and my family."
Combined with his time running Safeway, Magowan said he's spent "29 years in a true pressure-packed environment."
Magowan, one of the more public owners in baseball, was mentioned in the Mitchell Report that came out in December. Magowan then met with commissioner Bud Selig during spring training about whether members of the Giants' front office knew players were allegedly using steroids and performance-enhancing drugs.
Magowan said Friday he doesn't believe Mitchell included the Giants' side of the story in his report.
"I don't like my name put out there like it was," Magowan said. "The Mitchell thing, there's another side to all of this that has never come out. I had an opportunity to give that side, and I gave it to a good man. It didn't come out. ... The damage has already been done."
The decision to bring Bonds to San Francisco came soon after Magowan bought the team before the 1993 season. The Giants were close to moving to Florida before Magowan's group bought the team from Bob Lurie.
"Peter Magowan will always be remembered in the San Francisco Bay area for saving baseball in 1992 and for preserving the game for the next two generations of San Francisco fans by building the beautiful ballpark by the bay," Selig said. "During his 16 years with the Giants, he has made a great impact in the community and within the game. Personally, I will miss Peter. I will miss his wisdom and his counsel. I am grateful, though, that he leaves the ballclub in the very capable hands of Bill Neukom."
The addition of Bonds revitalized baseball in San Francisco and contributed to the opening of the franchise's privately funded waterfront ballpark in 2000. Last summer, the Giants hosted the All-Star game.