Jacob deGrom started for New York and punched out 13 Braves across seven one-run innings. He was followed by Seth Lugo (four K's), Edwin Diaz (two), Luis Avilan (one), Brad Brach (one), Paul Sewald (one), Justin Wilson (one) and Jeurys Familia (three).
DeGrom also provided the Mets' only offense with a solo homer in the sixth to level the score after MVP candidate Freddie Freeman gave the Braves the lead with an RBI single.
Billy Hamilton, who was claimed off waivers by Atlanta from the Kansas City Royals on Monday, played the role of hero with an RBI single in the 14th.
The loss dropped the Mets 10 games behind the East-leading Braves.
New York and Atlanta have two games left in the weekend series at Citi Field. Zack Wheeler will try to pick up where deGrom left off for the Mets on Saturday, while Max Fried takes the hill for the Braves.