Medlen (10-10) notched his fourth win in four starts, limiting the Phillies to five hits and a walk while striking out five in a 93-pitch performance.
The hurler broke a scoreless tie with two outs in second inning when he ripped a 3-2 pitch from Philadelphia starter Ethan Martin over the head of right-fielder Darin Ruf, sending home Tyler Pastornicky.
David Carpenter hurled a scoreless eighth and Craig Kimbrel collected his 37th save as the National League East-leading Braves improved to 10-2 in August and evened their three-game series.
Chris Johnson bashed a two-run homer in third to provide what turned out to be the winning runs.
Martin (1-2) was touched for three runs on six hits over five full innings.
Chase Utley went 3-for-4 and Domonic Brown supplied an RBI for the Phils.