Kennedy (8-12) gave up two runs and two hits in 6 2/3 innings.
''Overall, a terrific outing,'' Padres manager Pat Murphy said. ''Another one where he can say he pitched well and gave us a chance.''
Kennedy has a 2.30 ERA this month with hitters batting .195 against him. He pitched well after walking three batters in the first inning.
''I felt a lot better after that and gave the team a chance,'' he said.
The Phillies took a 2-1 lead with a pair of runs in the fourth. A hit batter and a pair of singles loaded the bases with no outs.
After Cody Asche popped out, Rupp brought home a run with a groundout and Ryan Howard scored the go-ahead run from third on a wild pitch.
Justin Upon had given San Diego a 1-0 lead with his 23rd homer of the season in the top of the frame.
The Phillies broke open the game with five runs on four hits in the eighth off relievers Mark Rzepczynski and Odrisamer Despaigne.
''We had a little blip in the eighth,'' Murphy said.
Aaron Altherr tripled, Rupp hit a three-run homer and Jeff Francoeur had an RBI double, his major-league leading 11th pinch-hit RBI.
''Give credit to the Phillies, but we're hoping to win the series,'' Murphy said.
Nola (5-1) allowed one run and two hits, striking out six. The righty has permitted one run and five hits in his last two starts over 15 innings.
He watched from the dugout as the Phillies were outscored 40-21 in a four-game sweep by the New York Mets this week.
''After seeing that, it makes me want to go out there and have a good start,'' Nola said.
Phillies interim manager Pete Mackanin added: ''I'll take five starters like him. He really knows what he's doing.''
Altherr has seven hits in the majors, all for extra bases.
''I hope he does that the whole year,'' Mackanin joked.
Jerome Williams pitched two perfect innings to earn his first save. He was moved to the bullpen prior to the game to make way for righty Alec Asher, who will start on Sunday.
''Just helping out the team any way possible,'' Williams said. ''It was fun, wasn't nerve racking or anything.''
Rupp is batting .333 with six homers and 17 RBIs in his last 17 games.
''I'm just getting good pitches to hit when balls are in the zone,'' he said.
EXTRA BASE MAN
In eight games, Altherr is 7 for 29 with four doubles, a triple and two homers.
''I'm just fortunate they're going for extra-base hits,'' he said. ''I'm ready to be in there and show what I can do.''
Padres OF Matt Kemp (sore left shoulder) missed his second straight game after getting injured diving for a ball on Wednesday in Washington.
''He's our guy,'' Murphy said. ''He makes our offense go and makes everybody else better.''
Kemp has reached base in 17 straight games while batting .338 with four homers and 19 RBIs over that stretch.
IN A PINCH
Francoeur is batting .478 as a pinch-hitter this season after entering the year hitting .138 in the role.
Phillies: LHP Elvis Araujo was put on the 15-day DL after straining his left groin delivering a pitch on Thursday night. Philadelphia recalled RHP Nefi Ogando from Triple-A Lehigh Valley.
Phillies LHP Adam Morgan (4-4, 4.43) opposes San Diego RHP Colin Rea (2-1, 5.52) in the second game of the three-game set on Saturday night. Morgan earned the win in Philadelphia's 4-2 victory at Petco Park on Aug. 8 when he allowed one earned run in six innings.