Bobby Parnell blew his first save since taking over for regular closer Frank Francisco, when he gave up three runs in the eighth inning to cost New York its lead.
The Braves scored all three times with two outs, with RBI singles by Michael Bourn, Martin Prado and Jason Heyward in succession.
Despite a mediocre outing from R.A. Dickey, the Mets were able to take the lead in the sixth after trailing throughout the game. Justin Turner, Ruben Tejada and Jordany Valdespin singled in runs to take a 6-5 lead and kept Dickey in line to attain his 13th win of the season.
Dickey's final line was five runs allowed on eight hits and two walks in five innings. He also struck out four.
Andres Torres had the best day at the dish for the Amazins'. Torres went 3-for-4 with two runs scored and an RBI.
On Sunday, New York will try to avoid the sweep at Turner Field when Johan Santana takes the hill against Ben Sheets, who's making his first appearance as a Brave.