Freddie Freeman came off the bench to hit a two-run double and game-winning three-run homer Wednesday night, reclaiming his status as Atlanta’s best Mets-killer since Chipper Jones, and giving the Braves their second consecutive series win.

Out of the lineup with a sore wrist, Freeman entered to hit a pinch-hit, two-run double to put the Braves ahead in the seventh inning, then broke open a tied-again game in the ninth when he crushed an opposite-field homer off Mets closer Jeurys Familia for a 6-3 win in a series finale at Citi Field.

“Unbelievable, man,” said Braves center fielder Cameron Maybin, who singled and was driven in by Freeman in both the seventh and ninth innings. “What a day off the bench. That’s the kind of things that he’s capable of doing. That’s the reason why this organization signed him to a long-term deal. Whenever he has that going, we can do some special things.”

The Braves have won five of their past six games, but consecutive wins against the National League East-leading Mets gave them their first series win in six weeks against a team other than the last-place Philadelphia Phillies, the only major league team with a worse record than the Braves (62-91).

They have nine games left, and Freeman just hopes his troublesome right wrist will allow him to help win more of them.

“The wrist has been bothering me for a couple of weeks now and it’s gotten progressively worse,” said Freeman, who spent 6 1/2 weeks on the disabled list in June and July with a sprain and bone bruise in the wrist. “It’ll be playing through pain for the next nine days, but it’s just, got to muster up and play through it.

“I told Skip (manager Fredi Gonzalez) before the game, if a big situation comes up I’ll go out there and hit. Obviously it came up in the seventh inning.”

Gonzalez said before the game that Freeman would be available if needed in the late innings.

“We were just going to try to take it easy on him, give him two days, but obviously our training staff did a terrific job,” Gonzalez said. “Gave him enough time to get him warmed up when we had to use him. He did treatment in here all day, didn’t take batting practice, just hit off the tee in the cage before he came out in the seventh inning to pinch-hit.”

After sweeping the Phillies at home last weekend, the Braves started their final road trip with a 2-1 series win, and will have a day off Thursday Miami before beginning a three-game series against the Marlins on Friday.

They came back to beat the Mets after falling behind 2-0 through two innings and not having a runner reach base against Mets starter Bartolo Colon until Jace Peterson’s tw0-out infield single in the fifth.

“You play 27 outs for a reason,” Maybin said. “And we continue to fight, continue to battle, continue to pick each other up. Those are things that we’re looking to do going into 2016 and finishing this year right.”

Freeman’s status could play a big factor in whether they continue this momentum through the remaining games.

In 55 games against the Mets during the 2012-2014 seasons, Freeman hit .325 with 18 doubles, 12 homers, 51 RBIs and a .580 slugging percentage. But in 15 games against them this season before Wednesday, he was 11-for-58 (.190) with two homers, five RBIs and a .293 slugging percentage.

In one night, with two late-innings swings, he reminded the Mets and their fans of what a force he can be.

“Freddie is a thorn in our side,” Mets third baseman David Wright said. “I wasn’t expecting to see him tonight. He comes off the bench and kills us again. So I’ll be glad to get rid of him and Andrelton Simmons and everybody else that beats us up over there. Freddie came in and singlehandedly beat us tonight. That why he is who he is. It just seems like he elevates his game against us.”

Colon took a perfect game into the fifth inning and a two-hit shutout through six, before the Braves flipped the script in a three-run seventh that started with three singles to load the bases and chase Colon from the game.

Michael Bourn greeted reliever Addison Reed with an RBI single and Freeman’s double gave the Braves a 3-2 lead.

“It’s been a frustrating season in all areas for this team, and for me personally it’s been injury-plagued, and it looks like it’s going to end injury-plagued,” Freeman said. “So to be able to come off the bench and help this team win, it’s definitely a good feeling ….

“Going to have to probably go in there and see what’s going on with an MRI again, probably after the season. It’s just a lot of pain. Just one of those things that went away for about three weeks and came back, after I came back (from the DL).”

Braves starter Williams Perez wiggled out of a few tight spots to work six innings, allowing seven hits and two runs with one walk and two strikeouts. He gave up a two-out homer to Daniel Murphy in the first inning, and a run on three hits in the second including Lucas Duda’s leadoff double and Wright’s RBI single.

Wright tied the game in the seventh with a two-out single off reliever Brandon Cunniff, after Ruben Tejada singled off rookie Matt Marksberry to start the inning. Four of five pitchers used by the Braves were rookies – Perez, Cunniff, Marksberry, and closer Arodys Vizcaino. Veteran Edwin Jackson got some big outs in the eighth inning.

Before Wednesday, Colon was 4-0 with a 3.51 ERA in four starts against the Braves this season.

Russell replaced Colon and fell behind 3-1 against the first batter he faced, Bourn, who tossed his bat and headed to first base after the next pitch, sure that it was ball four. It was called a strike, and Bourn, in disbelief, retrieved his bat, stepped back in the box and drove the next pitch for an opposite-field single that cut the lead in half, 2-1.

After Freeman came within a few feet of a grand slam, Braves had a chance to blow the game open after the Mets intentionally walked Nick Markakis to reload the bases for Hector Olivera, who grounded into an inning-ending double play.

Colon got no decision and was charged with five hits, three runs and one walk with one strikeout in 6 1/3 innings. The portly right-hander is 8-0 this season in nine starts against the Braves and Phillies, 4-2 in six starts against the Marlins, and 2-10 against everyone else.