The plan was to rebuild the Mets through pitching. In Tuesday night’s nightcap, when Zack Wheeler debuted on the day that Matt Harvey flashed brilliance in the opener of a doubleheader, it seemed that the Mets’ plan was finally falling easily into place. Less than 48 hours later, those plans were temporarily put on hold.

Jon Niese, the Mets’ only left-handed starter, was forced to leave Thursday night’s game in the fourth inning with “left shoulder discomfort.”

The Mets bullpen didn’t allow a run the rest of the way, with Bobby Parnell wrapping it up with his 11th save of the season and David Wright blasted two home runs as the Mets beat the Braves, 4-3, at Turner Field.

The Mets (28-41) won their third game in four days and won a series for the first time since taking four from the Yankees in the last week of May. It also was the first time the Braves (43-31) had lost a series at Turner Field this season.

The win proved costly, however, as Niese, who missed a start at the beginning of the month because of tendinitis in his left shoulder, said he felt pain and weakness in his shoulder while facing his second batter of the fourth inning. He will fly to New York on Friday morning to be examined by team doctors, but after an initial physical exam in the clubhouse, Niese was optimistic.

“Not really much,” said Niese, referring to what was found in his shoulder. “It’s never good when you have to leave the game, but the doctors did some tests and everything was negative,” Niese said. “It just felt very weak. I think the tendinitis flared up again. I am going to go back to New York, and hopefully everything is all right.”

Niese said he felt fine in the first three innings, but after a flash of pain and one diminished fastball, he called for the trainer. Compared to his tendinitis in the past, Niese said the pain was not as bad. He added that once he got back into the clubhouse it calmed down.