Freeman supplied a two-run double in the first inning to open the scoring and added a three-run homer in the second for 6-1 Atlanta lead.
Schafer contributed a run-scoring single while Andrelton Simmons chipped in with three RBI as the National League Central-leading Braves took the opener of a three-game series.
Paul Maholm (10-10) went five innings for the win, allowing three runs on six hits. He walked three and struck out four.
Mets starter Daisuke Matsuzaka (0-3) was raked for six runs on seven hits in a three-inning effort.
The hurler also drove in a run with an second-inning single for New York.