Lee (5-1) was making his sixth start with Philadelphia since being traded from Cleveland on July 29.
Matt Diaz and Yunel Escobar also homered off Lee, who had been practically unhittable for the NL East-leading Phillies entering Saturday night. He entered with an ERA of 0.68 and had surrendered just 24 hits and six runs, three earned, in 40 innings while holding opponents to a .175 average.
After three scoreless innings, Anderson gave Atlanta a 3-1 lead in the fourth with his three-run shot to right. Four batters later, Diaz hit a two-out, two-run homer.
In the next inning, Yunel Escobar homered to deep left to make it 6-1.
Prior to the Braves' power surge, Lee hadn't allowed a homer in 43 innings since being traded to Philadelphia. The three homers he gave up Saturday were the most allowed in a game this season by Lee, who had surrendered just 10 in 192 innings entering Saturday. He left after giving up 10 hits and six runs in five innings.
Derek Lowe (13-9) scattered eight hits in 5 2-3 innings, striking out five, to improve to 6-1 lifetime against the Phillies and 4-0 at Citizens Bank Park.
Anderson and Diaz finished with three hits, while Escobar had two hits.
Chipper Jones hit a two-run homer in the sixth. He had been in a 3 for 42 skid.
Philadelphia's Chase Utley hit a solo homer in the first, his 28th of the season.
NOTES: Anderson is 10 for 20 in his career against Lee with eight RBIs. ... Braves 1B Adam LaRoche left with an aggravated right hamstring after batting in the fourth inning. ... Diaz has 19 hits in his last 31 at-bats.