Shane Victorino singled to start the seventh for the first hit off Lowe, and Placido Polanco followed with a double. The right-hander then came out of the game with an apparent leg or foot injury.
Lowe (3-3) appeared to hurt himself in the top of the seventh after singling and going to second on Chipper Jones' single.
Brian McCann had a pair of doubles and an RBI, and Alex Gonzalez had three hits and an RBI for the Braves.
Lee (2-3) set the major league high for strikeouts this season, coming within one of the franchise record.
The big league mark for a nine-inning game is 20.
Trailing 3-0, Lee was pulled after throwing 117 pitches, 87 strikes, in seven innings.
Braves batters finished with 18 strikeouts, tying a club record for a nine-inning game. The last time it happened was May 22, 2006, at San Diego.
Lowe, who threw 97 pitches, limped off the mound after striking out four and walking one.
Despite not allowing a hit to that point, the Braves had relievers warming up in the bullpen at the start of the seventh. Facing Victorino to open the inning, Lowe got two strikes on the Philadelphia batter when he trotted off the mound toward second base, apparently trying to walk off his injury. Victorino broke up the no-hit bid with a clean single to left on the next pitch.
Atlanta trainers visited the mound before Philadelphia's next batter, Polanco, and manager Fredi Gonzalez lifted Lowe after Polanco doubled to center to put runners on second and third.
Left-hander Eric O'Flaherty came on in relief and struck out the side to end the threat. Jonny Venters and Craig Kimbrel each worked an inning to complete the two-hitter.
Lowe was trying for his second no-hitter. As a member of the Boston Red Sox, he stymied Tampa Bay in a 10-0 win on April 27, 2002, at Fenway Park.
Lee struck out 16 of the 30 Braves he faced in a dominating performance marred by four consecutive hits in the third inning that resulted in three Atlanta runs. The 16 strikeouts were one shy of Art Mahaffey's 17, set on April 23, 1961, for Philadelphia against the Cubs.
The last Phillies pitcher to have 16 strikeouts in a game was Curt Schilling, who did it on Sept. 1, 1997, against the Yankees. Philadelphia's Chris Short struck out 18 on Oct. 2, 1965, against the Mets in a 15-inning game.