Kennedy struck out five, giving him 201 for the season.
''You set little goals,'' he said. ''I've never had it before. It's one of the goals that sometimes you can control. I was a little more efficient than I have been. They were very aggressive early on.''
He joins Kevin Brown (257, 1998), Jake Peavy (240 in 2007, 216 in 2005 and 215 in 2006) and Clay Kirby (215, 1971).
''There are some really good pitchers in that group,'' Kennedy said. ''To be in the company with those guys is an honor. Peavy had such great years here and Kevin Brown was awesome, too.''
Peavy, traded from San Diego to the Chicago White Sox in 2009, is now with the Giants.
Kennedy (12-13) held the Giants to two runs and five hits in 6 2-3 innings, with one walk.
Kennedy retired the first 11 Giants batters before Buster Posey beat out an infield single.
''Ian was steady,'' manager Bud Black said. ''Right out of the chute, he was pitching very aggressive with the fastball. He was throwing the fastball with a lot of conviction.''
The Giants' chances of winning the division were dealt a serious blow by the three-game sweep at the hands of the lowly Padres. The Giants open a three-game series at Dodger Stadium on Monday night.
San Francisco is still in good shape to clinch a wild-card berth, although it dropped into a tie with Pittsburgh in the race for the top spot. The Giants and Pirates are 4 1/2 games ahead of Milwaukee.
San Francisco has scored only 14 runs in losing six of eight games.
Yasmani Grandal had three RBIs while Rene Rivera and Cameron Maybin each drove in two runs for the Padres, who improved to 9-6 against the Giants this year. The teams will finish the season with a four-game series in San Francisco starting Thursday night.
Ryan Vogelsong (8-12) held the Padres hitless until Seth Smith doubled into the gap in right-center leading off the fifth. Smith advanced on Rivera's single to left and scored on Amarista's sacrifice fly.
The Padres piled on in the sixth with four runs, three unearned, off three pitchers.
Yangervis Solarte and Will Venable singled opening the sixth and a throwing error by third baseman Pablo Sandoval on Jedd Gyorko's grounder loaded the bases and chased Vogelsong. Javier Lopez allowed a sacrifice fly by Grandal and walked Seth Smith to again load the bases. George Kontos came on and allowed Rivera's RBI groundout. Alexi Amarista was intentionally walked and Maybin hit a two-run single.
Grandal hit a two-run double in the seventh.
Vogelsong allowed four runs, two earned, in five innings while striking out five and walking one.
Giants rookie Chris Dominguez hit a two-run homer to left off Kennedy with two outs in the seventh for his first career big league hit. He was called up from Triple-A Fresno on Sept. 1. Brandon Crawford was aboard on a single.
Giants: Manager Bruce Bochy said it's doubtful that CF Angel Pagan and INF-OF Michael Morse will be able to play in the Dodgers series. Pagan has a bulging disc in his back and will be examined again on Monday. Bochy said Morse likely will go to San Francisco to get an MRI on his strained side muscle.
Padres: Black isn't sure if RHP Tyson Ross will make another start this season due to a sore right arm. Ross last pitched on Sept. 13.
Giants: RHP Jake Peavy (6-4, 2.16 ERA) will make his 11th start with Giants when they open a three-game series against Dan Haren (13-11, 4.14) and the Dodgers in Los Angeles.