Mets starter Dillon Gee had carried a three-hit shutout into the ninth inning while clinging to a 1-0 lead, but that's where it fell apart for New York.
Justin Upton reached him for a one-out single and Freeman followed by smacking a pitch into the fourth row of the bleachers in right field, handing the Braves a win in a game that began 3 hours, 43 minutes late due to rain.
David Carpenter (1-0) was credited with the win after tossing a scoreless top of the ninth.
Braves starter Tim Hudson had held the Mets to one run on six hits over seven full frames.
Gee (5-7) was tagged with the hard-luck loss after surrendering just Freeman's homer in an 8 1/3-inning complete-game defeat. The right-hander allowed one walk and struck out six.
He also drove in the Mets' only run with a seventh-inning single as New York fell in the opener of a five-game series against the National League East leaders.