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 inning of the Braves’ 3-2, 10-inning win over on the Mets on Sunday, 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 Sunday to give the Braves their fifth straight win — and 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.

“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.

The Mets took the lead on Davis’ RBI single in the fourth, but Atlanta answered when Bourn singled home Jose Constanza in the fifth.

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.

Hanson’s day ended when David Wright hit a double into the left-field corner to tie it at 2 in the sixth. It started off with more promise — Hanson retired the first 10 batters he faced.

“I felt really good about this start today,” Hanson said. “We came up here and took care of business.”

In the bottom of the eighth, the Mets threatened to take the lead.

But Braves reliever Eric O’Flaherty got Wright to ground out on a full count with two outs in the bottom of the eighth and runners on first and third.

That set up Jones’ moment, such that it was. Reliever Frank Francisco walked him on four pitches.

“I didn’t want to pitch around him, but I didn’t want to leave anything right there,” Francisco said about the at-bat.

“He’s a great player. I was trying to save the game.”

Jones noticed, too.

“I don’t think Francisco was going to let me get a real good swing at one,” Jones said.

As much as he might have liked to have one last good whack at the Mets, Jones was pleased enough with the actual results: Atlanta goes to Milwaukee with a three-game sweep and having won seven of its last eight.

And Jones has one more memory of a Mets ballpark. He hit the first two homers of his career at the Mets’ old stadium, and his eight-year-old son is named for it — Shea.

“It was cool,” Jones said of his last at bat in Queens, nearly 20 years after his first one. “I heard a bunch of boos in there, but for once the cheers outnumbered the boos.”

BRAVES NOTES:

l Jones will get another chance to torment the Mets. The Braves host them in a series later this month.

l Mets right-hander Colin McHugh is scheduled to face the Nationals Gio Gonzalez today at Citi Field.

McHugh, a former Berry standout, was recalled when the roster expanded to 40 on Sept. 1.

This will be McHugh’s third start in the big leagues this season, and he is 0-1 with a 3.27 ERA with 11 strikeouts in 11 innings pitched.

He pitched seven scoreless innings in his debut for the Mets but go no decision.