The 117 games played by the Padres marks the furthest a team has been into a season and still be in first place with a record under .500.
In addition to losing the game, the Padres also lost shortstop Khalil Greene, who sustained a displaced fracture of the left big toe when he dove for a ground ball on a base hit by Todd Pratt.
Padres manager Bruce Bochy said that Greene would be reevaluated at Scripps Hospital on Monday and will likely be out from two to three weeks.
Bochy acknowledged that the loss of Greene is a "big blow" as the Padres head out on a six-game road trip with three games against the Marlins and three against the Braves.
"It's getting old getting swept, there's no getting around it," said Bochy, whose Padres have been swept seven times this year, including twice by the Phillies. "It's not fun getting swept and the Phillies have had our number this year. We have to stop that from happening."
Phils rookie Robinson Tejeda (3-2) went seven innings, allowing three hits and one run, a homer by Brian Giles in the fourth. He walked three and struck out seven.
Chan Ho Park, who is 1-1 with the Padres, took the loss, giving up six runs (five earned), walking three and striking out four in four-plus innings.
Giles had tied the game at 1 in the bottom of the fourth when he hit his 12th home run over the right-field wall.
However, the Phillies bats, coupled with two Padres errors, opened the floodgates in the top of the fifth. Philadelphia sent 12 men to the plate, with nine reaching base safely.
"We just gave them too many outs in that fifth inning," Bochy said. "We broke down there. We actually had [David Bell] at third base on that bunt, but [Miguel] Olivo threw it away. And that kind of set up the big inning."
Bell singled and Pratt walked to start the rally. Tejeda dropped down a bunt. Olivo picked up the ball and threw wildly to third trying to get Bell. The ball sailed into left field with Bell scoring to make it 2-1.
Jimmy Rollins got an infield single to load the bases. Kenny Lofton singled to left, scoring Pratt, and that was all for Park.
Chase Utley greeted reliever Clay Hensley with a two-run single before Padres second baseman Eric Young threw wildly to second on a potential double-play ball hit by Bobby Abreu.
Pat Burrell delivered a two-run single and Ryan Howard an RBI single before Hensley got Bell on a popup to third for the first out. That got the loudest cheer of the day.
San Diego scored a pair of runs in the eighth on Ryan Klesko's bases-loaded groundout and wild pitch by Phils reliever Rheal Cormier.
Neither Bochy nor the Padres wanted to dwell too much on this lost weekend, preferrring to look ahead.
"We're going against good teams and very good pitching on this road trip with Florida and Atlanta," said Bochy. "And hopefully the same things happens that happened the last road trip, and we can get back to putting runs on the board playing good baseball."
The Padres went 5-1 on their last road trip, scoring 44 runs in winning two of three from Pittsburgh and sweeping Washington.