Freeman, who had two homers in Atlanta’s 4-1 win in Monday’s series opener, hit his 12th homer to center field off Jhoulys Chacin in the second inning.
Lowe (5-6) gave up three runs and five hits in 5 1/3 innings and pushed the lead to 4-0 with his bases-loaded double in the fourth. Lowe’s hit drove in Chipper Jones, who doubled, and Dan Uggla and Nate McLouth, who both walked.
Uggla added his 13th homer in the sixth.
The Rockies outhit the Braves 9-7 but had no extra-base hits as Carlos Gonzalez and Troy Tulowitzki were held out with injuries.
Craig Kimbrel pitched the ninth for his 26th save for the Braves, who have won seven of their last eight.
Chacin (8-6) matched his career high with six walks for the second time in his last three starts. He gave up four hits and four runs in five innings.
Mark Ellis had three hits, including an eighth-inning single to give the Rockies runners on first and second. Ian Stewart’s groundout advanced the runners before Jonny Venters struck out Chris Iannetta and Jason Giambi — each on called third strikes — to end the threat.
Stewart, recalled from Triple-A Colorado Springs to begin his third stint of the season with the Rockies, started at third base and was 0-for-3 with a walk and a run scored.
Gonzalez missed his second straight game after he bruised his right wrist Sunday. Tulowitzki was held out after leaving Monday night’s game with a strained quadriceps. Neither player is expected to be placed on the disabled list.
A groundout by Chacin and Charlie Blackmon’s run-scoring single helped Colorado pull within 4-2 in the fifth. Ianetta added a run-scoring single in the sixth.
Uggla was hitting .173, including walks in his first two plate appearances, before he pulled left-hander Eric Stults’ first pitch deep into the seats in left in the sixth. He added a double in the eighth.
NOTES: Braves OF Martin Prado could begin a rehab assignment today if given the go-ahead from his physical therapist. Prado has been out since June 8 with a staph infection in his right calf. ... Lowe has five hits this season, including three doubles. ... Rockies OF Cole Carner was optioned to Colorado Springs after only one game with the Rockies. ... Jonathan Herrera, who filled in for Tulowitzki, had two hits. ... Lowe posted his 1,600th career strikeout against Seth Smith in the second.