Kendrick (3-2) shook off a shaky first inning and allowed three runs and six hits. Lidge finished for his 10th save in as many chances, though he allowed his first earned run of the season.
Chipper Jones went 3-for-4 for the Braves, raising his major league-leading average to .415.
Lidge hadn't allowed an earned run in 17 2/3 innings before Brian McCann hit an RBI double with two outs in the ninth. Werth completely misplayed the liner to center, breaking in and allowing the ball to sail over his head.
"I read the swing, the crowd was yelling and I wasn't able to hear the contact," Werth said. "It was a one-handed swing. I read in all the way. It was definitely a miscue. You learn from it."
Trailing 3-0, the Phillies rallied against Jo-Jo Reyes (1-1) in the fourth. Chase Utley singled to start the inning and Ryan Howard lined a double to center. Werth, who was 3-for-4, ripped a one-out single to center to cut it to 3-2.
Werth blooped a single to left that scored pinch-runner Eric Bruntlett with two outs in the seventh for an insurance run.
"I haven't been hitting well with guys on base," Werth said. "I'm glad I got the guys in when it counted."
Reyes gave up five runs and 11 hits in 6 2/3 innings.
"I think this was the best I've thrown up here," Reyes said. "My command was the key. I didn't walk anybody and I was locating my fastball."
Werth played center for the first time since Victorino returned from the disabled list. Victorino started in right, though manager Charlie Manuel isn't planning to make a permanent switch.
"He made a mistake, but he can correct that," Manuel said about Werth misjudging McCann's hit. "I said before the season I wanted Werth to play some in center. I played him there tonight because it was time to give him some time there."
Jones had an RBI single in the first and Francoeur's two-run single gave the Braves a 3-0 lead.
"I fell behind and left some pitches up," Kendrick said. "With the offense we have, you just have to keep it close."
A sellout crowd of 44,101 broke into a "Let's Go Flyers" chant several times throughout the game. The NHL's Philadelphia Flyers played the Pittsburgh Penguins across the street in Game 3 of the Eastern Conference finals, but lost 4-1.
Braves 1B Mark Teixeira missed his second straight game with back spasms. He might return Wednesday. ... The Phillies are 16-1 when leading after eight innings. ... Atlanta's Tom Glavine (0-1) seeks his first win Wednesday night. He'll face Brett Myers (2-3). ... Jimmy Rollins snapped an 0-for-13 slump with a double in the eighth. ... Werth's four RBIs tied a career best.