Santana (11-7) threw 115 pitches with two walks and five strikeouts before he was replaced by reliever Pedro Feliciano.
Angel Pagan led New York with three hits and one RBI. Former Brave Jeff Francoeur had two hits and one RBI for the Mets, who have won only six of their last 19 games.
Atlanta's run scored in the eighth on a homer by Chipper Jones, his 10th this season. Casey Kotchman had two of the eight hits for the Braves, who had won six of eight.
Losing pitcher Kenshin Kawakami (5-7) surrendered two runs and five hits in 6 2/3 innings.
Copyright 2009 by United Press International.