Both clubs rolled out pitchers who are not expected to make the starting rotation when the season begins.
Freeman homered in the seventh inning and again in the ninth, giving him five homers in exhibition play. Bourn hit a three-run homer drive off Mets starter Chris Schwinden.
Lucas Duda homered for the Mets and David Wright, in the lineup for a second straight day after making his spring debut Monday, had a sacrifice fly.
Braves starter Buddy Carlyle gave up two runs and three hits in four innings.