Holm homered in his first at-bat on the first pitch he saw from J.C. Romero (3-1) after replacing Bengie Molina in the top of the seventh, sending the ball into the seats in left-center. Romero had allowed only one homer in his previous 61 appearances and came in with an 0.63 ERA over his first 17 outings of 2008.
Jack Taschner (2-0) pitched the seventh for the win, Tyler Walker worked a 1-2-3 eighth and Brian Wilson finished for his 11th save in 13 opportunities. San Francisco rallied for its first series win this month in three chances.
The Phillies went ahead 3-2 in the fifth when Pat Burrell hit a sacrifice fly after Ryan Howard's first triple of the year. Howard's hit drove in a run and chased San Francisco starter Jonathan Sanchez.
Phillies starter Adam Eaton drew a bases-loaded walk in the fourth to tie it at 1.
The Giants snapped a season-long five-game losing streak with an 8-2 victory Saturday, then managed just enough offense Sunday. San Francisco hadn't won a series since beating the Rockies two out of three at home to end April, including dropping two of three in Philadelphia from May 2-4.
Reigning NL MVP Jimmy Rollins went 0-for-5 in his third game back from a disabled list stint with a sprained left ankle. He had three hits Friday in his return, missing the cycle by a triple.
The Bay Area native from nearby Alameda used a pink bat with his mom's name on it - Gigi - for Mother's Day and breast cancer awareness. She was once a standout middle infielder for the Allen Temple Baptist Church women's fast-pitch softball team.
"My mom never made outs," Rollins said before the game.
San Francisco's Ray Durham struck out as a pinch hitter to leave the bases loaded in the sixth, and the Giants missed several other scoring opportunities.
John Bowker singled in a run in the second to give San Francisco a 1-0 lead, but Jose Castillo followed by grounding into an inning-ending double play. The Giants hit into double plays again in the third, fourth and sixth innings - Castillo doing so in the fourth and sixth.
Omar Vizquel was intentionally walked three times in the eighth hole to bring up the pitcher, but Durham pinch-hit in the sixth. That's after Vizquel got three hits in his season debut Saturday, when he returned following Feb. 27 arthroscopic surgery on his left knee.
The intentional free passes were the most by a Giant since indicted home run king Barry Bonds drew four against Houston on Sept. 22, 2004.
San Francisco left-hander Barry Zito (0-7) will try again for his first victory of the season Monday when the Giants face Astros ace Roy Oswalt in the opener of a four-game series with Houston.
Notes: The Phillies began a stretch in which they are scheduled to face four lefty starters in a row. ... Giants RHP Kevin Correia, nursing a strained muscle in his left side, hopes to be throwing off a mound again in about a week. ... Sanchez made his first career start vs. Philadelphia. ... San Francisco 1B Dan Ortmeier celebrated his 27th birthday. Zito turns 30 on Tuesday.
