"Good games -- I'm proud of the way we played," said Padres manager Bud Black. "That's a tremendous team over there [the Giants]. They have experience, they have All-Stars.
"But we play hard. That's a good series for us. I'm happy for the guys."
For the third time in as many days, the Padres (74-81) got another strong performance from a starting pitcher, as Ian Kennedy (12-13) took a three-hit shutout into the seventh inning before eventually allowing a two-run home run to Chris Dominguez for his first big league hit.
"I executed pitches," said Kennedy, who allowed two runs on five hits in 6 2/3 innings with one walk and five strikeouts. "I'm getting ahead of guys and staying on top of my fastball."
Kennedy's seventh-inning strikeout of Hunter Pence gave him a career-best 200 strikeouts and allowed him to become the first Padres pitcher to reach that mark since Jake Peavy did so in 2007, when he had 240 strikeouts. Peavy won the NL Cy Young Award that season.
Kennedy's start followed gems by Odrisamer Despaigne (seven shutout innings) on Friday and Andrew Cashner (two runs in eight-plus innings) on Saturday.
"We've pitched really well," Black said.
San Francisco pitcher Ryan Vogelsong (8-12) didn't allow a hit until Seth Smith doubled to start the fifth inning. That hit directly led to the Padres' first run, as Smith later scored on Alexi Amarista's sacrifice fly to center field, his eighth RBI during the first seven games of this homestand.
Leading, 1-0, the Padres added four runs in the sixth inning, two on outs -- a sacrifice fly by Yasmani Grandal and a ground-ball out by Rene Rivera. Cameron Maybin added a two-run single.
A throwing error in the inning by third baseman Pablo Sandoval led to two unearned runs.
The Padres added three more runs in the seventh inning, two on a double by Grandal and one more on a single by Rivera.
The Padres are now 46-32 at Petco Park this season.
"This is a tough place. They have a good staff and you have to play your best ball. We didn't do it. They outplayed us and that's the bottom line," said Giants manager Bruce Bochy.
Vogelsong allowed four runs, two earned, on four hits in five-plus innings. He walked one and struck out five.
Amarista saved a run from scoring in the fifth inning when he smothered a ball up the middle off the bat of Vogelsong that was headed into center field. Vogelsong was credited with a single but the Giants left the bases loaded as Gregor Blanco flied out to center field.
The Giants (84-71) are now tied with the Pirates for the Wild Card lead and will likely face each other Oct. 1, though if the teams end up tied, the Pirates -- who own the tiebreaker -- would host that game.