Chris Johnson went 2-for-3 with a solo homer and Schafer also went deep for National League East-leading Atlanta, which avoided a three game sweep.
Paul Maholm (8-6) corralled the victory despite yielding four runs on eight hits over five innings.
Four Braves relievers combined to toss three shutout frames and Craig Kimbrel earned his 21st save to secure the win.
Brewers starter Alfredo Figaro (1-2) was pounded for six runs on nine hits over just 3 1/3 innings.
Jonathan Lucroy clouted a two-run homer and Logan Schafer supplied two RBI for Milwaukee.