The Mets managed only two hits, but scored three times in the third on bases-loaded walks by winning pitcher Jair Jurrjens (3-2).
Jurrjens lasted six innings, overcoming four straight walks in the third as the Mets were taking a 3-1 lead.
Mike Pelfrey (2-1) absorbed the loss, giving up five runs on nine hits in 5 1/3.
New York has lost five out of six.
Atlanta Manager Bobby Cox was ejected in the third inning by home plate umpire Tim McClelland for arguing a bases-loaded walk to David Wright. It was Cox's 136th ejection, extending his major league record.