He departed to attend Harvard Business School and work for Westinghouse Broadcasting, then returned to the Giants to help form an ownership group that kept the team in San Francisco when it appeared to be headed to Tampa, Fla., in 1992.
Baer helped negotiate the blockbuster free-agent signing of Barry Bonds, then did much of the heavy lifting to pull off a privately financed stadium project that became a San Francisco landmark, AT&T Park. His titles have included limited partner, team president, executive vice president, chief operating officer and president of China Basin Ballpark Corporation.
And now, he has a seat at the MLB Owners Meetings.
"I'm proud of the fact in many ways," Baer said of his confirmation, announced Thursday at the conclusion of the Owners Meetings. "It's been a set of ideal circumstances. It really is a nice story, to be part of a front office that worked very hard together and now to be our representative here. I'm very proud of everybody."
Baer said his daily workload won't change dramatically.
"Our last two CEOs -- Peter Magowan and Bill Neukom -- were owner-operators," he said. "Now we're in the mold of a more traditional CEO structure, a career manager. I trained in the industry of sports and media. It's just another way. I'm not saying there's a right way or a wrong way. The Giants felt it was the right way to go.
"I'll be more involved in the MLB dealings than I have been, and to some degree on the field with the baseball staff, which Bill and Peter might have handled. I'll be responsible for our relationship with MLB. And we'll promote other people."
During Thursday's meeting, owners were briefed on the ongoing bankruptcy and planned sale of the Giants' archrivals, the Los Angeles Dodgers.
"It's very important that the Giants-Dodgers rivalry on the field thrives," Baer said. "For me, it goes back to Peter O'Malley. We always had a great relationship with him, and in 1992, he helped our drive to save the club. We just want the Dodgers to be in good hands. And it looks like it's on the path to resolution."