Bochy will retain the rest of his staff, including pitching coach Dave Righetti, bullpen coach Mark Gardner, bench coach Ron Wotus and third base coach Tim Flannery.
A change was expected after the Giants finished 71-91 -- their third consecutive losing season and their first time at the bottom of the NL West since 1996. They plan to have a younger roster next season.
"It's more a matter of taking a step back and seeing what hasn't happened the last couple years," general manager Brian Sabean said. "We'll see if we can get a different dynamic, and a better result. Joe and Willie are very loyal, and as professionals, they understand the process. I can't fault their work habits. They did everything they could do."
Both coaches were offered unspecified jobs within the organization. Sabean said he expected Lefebvre would stay on, though Upshaw could seek other major league opportunities.
Bochy inherited his entire staff with the exception of Flannery after the Giants hired him last winter; though Lefebvre and Sabean have ties going back to high school, the GM has said Bochy deserved the chance to hire more of his own people.
Sabean said he and Bochy would begin discussions about possible replacements today. Sabean also is mulling personnel changes in the baseball operations department, though top lieutenant Dick Tidrow is considered entrenched.
The Giants struggled with situational hitting last season, particularly late in games. Their .254 average ranked 14th out of 16 National League teams. Only the Washington Nationals scored fewer runs among NL teams.
Lefebvre, 51, had spent six seasons on the Giants staff, including the past five as hitting coach. The former big-league outfielder grew up in New Hampshire and played with Sabean at Concord High School, then at Eckerd College in Florida.
Upshaw, 50, spent his first season as a full-time major league coach since 1997, when he was the hitting instructor for the Toronto Blue Jays. Upshaw was the Giants' coordinator of minor league hitting from 2003-05 but spent most of the past three seasons with the big-league club.
In addition to helping Lefebvre, Upshaw coordinated outfield defense, which was a problem for the Giants this past season.
Contact Andrew Baggarly at firstname.lastname@example.org.