NEW YORK — Mets fans cheered the loudest for Chipper Jones once he was out of their ballpark for good.

When he took the lineup card to home plate before his last game in Queens, Jones got some scattered applause. When he pinch hit in the ninth, he received cheers in full voice — along with some boos, of course.

Jones walked, and once a pinch runner came in to replace him, the retiring 40-year-old star trotted back toward the Braves dugout on the third base side and Mets fans stood and cheered.

Jones took off his batting helmet, raised it to the crowd, and then was gone down the steps.

For that, and for his long career as a most worthy adversary, Mets fans stood and applauded.

“Can’t say enough about the fans in New York this year. They’ve been awfully supportive both in person, out on the field, on Twitter,” Jones said. “I’m very appreciative to them for that.”

He and the Braves, of course, couldn’t leave town without getting the better of the Mets one last time.

Brian McCann homered and drove in the go-ahead run in the 10th inning to give Atlanta its fifth straight win, 3-2 Sunday for a three-game sweep at Citi Field.

“Now that I’m scuffling a little bit, it’s important for someone else to be stepping up,” Jones said.

Pinch runner Reed Johnson made it to third before Michael Bourn struck out, flinging his bat and helmet in rage after the inning ended.

Martin Prado led off the 10th with a single against Bobby Parnell (4-4). After Jason Heyward grounded out, Freddie Freeman was intentionally walked. Dan Uggla worked a walk before McCann hit a sacrifice fly.

Peter Moylan pitched the bottom half for his first save of the season.

Craig Kimbrel (1-1), Atlanta’s usual closer, worked a scoreless ninth for the NL wild-card leaders. Braves manager Fredi Gonzalez said he wanted Kimbrel to face the Mets’ mid-lineup power threats, Ike Davis and Lucas Duda, in the ninth while it was tied.

“Today, it fell where the big boys were coming up,” Gonzalez said. “It worked out.”

Davis led off with a single, but Kimbrel struck out Duda and Kelly Shoppach before Andres Torres grounded out to end the threat.

Mets starter Chris Young allowed five hits and four walks in six innings, striking out seven. He is 0-4 in seven starts at Citi Field this season.

McCann led off the sixth with his 20th home run for a 2-1 lead, but Braves starter Tommy Hanson remained winless in five starts since a victory over Miami on July 30. He’s 0-3 since then and has only made it out of the sixth inning in one of those starts.