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.
Boston schools pull out free condoms over wrapping complaints
Ray Liotta sues skin care company over use of likeness