Omar Infante's sacrifice fly put the Braves up 3-2, capping a three-run eighth. Atlanta handed the Mets their eighth loss in 28 games, cutting their NL East lead to two games over Philadelphia.
New York is still three up in the loss column after the Phillies beat Milwaukee 7-3.
Mike Gonzalez closed it out with a perfect ninth and the Braves won a one-run game away from home for the first time since a 7-6 victory on Aug. 9, 2007, also at Shea Stadium.
Atlanta had lost 22 such games in a row this season and 29 overall -- the longest streak of its kind in major league history, according to the Elias Sports Bureau.
After ex-Met Mike Hampton kept the Braves close, Jeff Ridgway (1-0) worked a scoreless seventh to win his first career decision. Gonzalez gave a big fist pump after earning his 10th save in 11 chances.
Scott Schoeneweis (2-4) took the loss, allowing a single to his only batter.
Jonathon Niese gets his second major league start for the Mets in the nightcap, a makeup from Friday night's rainout. Jo-Jo Reyes was scheduled to start for Atlanta.
It was New York's second doubleheader in seven days and sixth this season, its most since playing eight in 1998.
Santana struggled with his command early but managed to keep Atlanta off the scoreboard and carried a 2-0 lead into the eighth.
Consecutive singles by Brian McCann and Yunel Escobar to start the inning chased Santana, 6-0 in 14 starts since his last loss June 28 against the Yankees. He left to a warm ovation and tipped his cap to the crowd.
Once again, New York's shaky bullpen couldn't hold a lead for the lefty ace. Schoeneweis gave up a single to Casey Kotchman that loaded the bases, and Francoeur grounded Brian Stokes' first pitch through the middle for a two-run single.
Josh Anderson sacrificed, pinch-hitter Greg Norton was intentionally walked and Infante gave Atlanta the lead with a sacrifice fly to left.
It was the seventh time in 31 starts with the Mets that Santana left with a chance to win only to have the bullpen blow it. Five of those collapses have come in the ninth inning.
Braves relievers Will Ohman and Jeff Bennett combined for a perfect eighth.
The Mets loaded the bases with none out in the fourth on two singles and a walk. Damion Easley hit an RBI single and another run scored when Brian Schneider grounded into a double play.
New York had a great chance to expand the lead in the sixth after loading the bases with none out again. This time, Hampton escaped unscathed.
The 2000 NL championship series MVP for the Mets, Hampton got Easley to ground into a 5-2-3 double play. Schneider was intentionally walked before Santana struck out.
Hampton was booed all afternoon. He jilted the Mets after their 2000 World Series run, leaving for a $121 million, eight-year contract with Colorado that expires this season.
Omar Infante, left, high-fives Jeff Francoeur (AP Photo/Julie Jacobson)
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