In the bottom of the 13th, the Padres loaded the bases twice on Giants closer Brian Wilson, who wriggled out of the jam allowing just one run, getting Tadahito Iguchi to ground into a forceout with the bases jammed for the final out.
That made Keiichi Yabu (2-1), the fifth of six Giants pitchers, the winner.
"[Molina] is a tough hitter and tough to put away," said Hoffman, who came on in the ninth with the Padres leading, 1-0. "I got a pretty good pitch down and in, and he hit it out.
"I didn't think I beat myself," said Hoffman, who now has two blown saves and two losses. "I think I threw pitches I wanted to accordingly. Sometimes you don't like to tip your hat, but he went down and got a good pitch.
"It was a pretty good pitch; Bengie's a pretty clutch hitter. He got deep into the at-bat, not necessarily deep into a hitter's count. He saw fastball and changeup, and when you see that, your odds increase and you're able to work both ends of the plate.
"I'm not going to second-guess the pitch. I was comfortable with it, but it obviously wasn't good enough."
"The game is hard sometimes," said Maddux, who threw seven shutout innings, allowing four hits and striking out five. "Right now, we're going through a tough stretch."
Asked about the 75 pitches he threw Wednesday night, Maddux acknowledged that he was "done" after the seventh inning.
"I didn't know if I had a little hangover from [Friday's 100-pitch game in Arizona], but more mentally than physically I was done," said Maddux. "Our bullpen is a huge strength of our team. And the guy went down and hit a good pitch tonight. Every now and then, you have to tip your hat."
The Padres, who have dropped seven of their last eight, lost a 22-inning game to the Rockies in their last game at PETCO Park last Thursday.
"It was a good ballgame, well pitched on both sides," said Black. "They got the hits at the end; we didn't. We had a couple of opportunities and they made some pitches."
Matt Cain, who like Maddux was coming off his worst start ever after giving up nine runs last Friday against Arizona, pitched seven strong innings for the Giants. He allowed one run, on an RBI single by Brian Giles in the fifth. He gave up five hits and three walks and notched seven strikeouts.
"Trevor has been through this before. I'm sure there's frustration on his part," Black said. "In that case, Bengie went down and got a low changeup, and Bengie's a good low-ball hitter. He hit a good low-ball pitch off of Cla [Meredith] in San Francisco. That ball didn't get down enough, but sometimes you have to tip your hat to the hitters."
"Our guys are battling hard and doing everything they can to score. We're hitting early, looking at tape. We're just not getting the hits, but they will come. We just need to cash in on our opportunities, and when we do that, we'll get the wins."