Although he had trouble throwing consistent strikes again, Wheeler (4-1) fought through a difficult first inning that included three strikeouts with runners in scoring position.
Since the day he was called up from the minors, the Mets (45-53) are 20-13.
"I'm starting to feel a little bit more comfortable with my mechanics. I've just got to trust my stuff and go after guys," Wheeler said. "I've just got to get ahead and start setting guys up. It's a lot easier when you do that."
Daniel Murphy and Marlon Byrd had three hits apiece to help the Mets gain a four-game series split. But the news wasn't all good:Eric Young Jr., a spark in the leadoff spot since arriving last month, was pulled with pain in his right knee.
Mets manager Terry Collins called it a strain, but Young didn't sound too worried. He said precautionary X-rays were negative and he hopes to play in Friday's day-night doubleheader at Washington.
"Just playing it safe," said Young, obtained on the same day Wheeler made his debut. "We didn't want to try to push it."
One day after top pitcher Tim Hudson sustained a season-ending ankle injury when Young accidentally stepped on him, the NL East-leading Braves caught another tough break.
This time, it was a missed call by the umpires that helped the Mets score three times in the sixth and led to the ejection of Atlanta manager Fredi Gonzalez.
Wheeler squandered a three-run lead by giving up homers to Dan Uggla and Freddie Freeman. But the prized rookie allowed only four hits in six innings after throwing 31 pitches in the first. He tossed six shutout innings in Atlanta to win his big league debut June 18.
"He's a work in progress. But I'll tell you one thing, everybody's right: The sky's the limit with him. He's got plus stuff. He's tougher than people give him credit for. He's going to be fine, but he's got to make some adjustments," Collins said. "I was very happy with the way he battled back and kept us in the game."
Opponents are batting .114 (4 for 35) against Wheeler with runners in scoring position and .162 (11 for 68) with men on base.
Freeman's long homer to center leading off the sixth tied it at 4, but Wheeler ended the inning with a double-play grounder and New York went right back ahead in the bottom half.
Andrew Brown, who replaced Young in left field, opened with a double against reliever Kameron Loe (0-1) and went to third on a wild pitch. Murphy singled through a drawn-in infield to give the Mets the lead.
"Guys are swinging the sticks like crazy right now. It's fun," Wheeler said.
David Wright followed with a drive to left-center that bounced up and hit the protective railing above the wall before caroming back onto the field. Center fielder Reed Johnson raised his arms, looking for the ground-rule double signal, but third base umpire Chad Fairchild ruled the ball in play.
Murphy scored and Wright pulled into third with an RBI triple before Gonzalez came out to argue. He took his protest to plate umpire and crew chief Jeff Kellogg before Fairchild finally tossed him.
Gonzalez headed toward the dugout, but then went back at Fairchild, now standing behind third base again.
"I don't think I needed a replay to know I was right," Gonzalez said.
Kellogg declined comment after the game, saying the umps had to catch a flight.
Buck added a run-scoring double with two outs to make it 7-4.
Young beat out an infield single to start a four-run third and scored on Byrd's single. Buck hit a two-run single with two outs to put the Mets up 4-1.
Acquired from Colorado in a trade, Young was very upset Wednesday night after breaking Hudson's right ankle when he inadvertently stepped on the pitcher at first base.
Hudson, the leader of Atlanta's strong pitching staff, will have season-ending surgery once the swelling subsides.
Collins said Young "tweaked" his leg on the play, and one day later the speedy outfielder was removed in the fourth inning.
Uggla trimmed it to 4-3 with a two-run shot off Wheeler in the fourth. It was Uggla's second homer in two days and 11th at Citi Field, the most by a visiting player.
Wheeler threw a fastball over Uggla's head in the first, and the Atlanta second baseman glared out at the mound before saying something to Buck.
"I told him, 'Look, you can be mad at him because he doesn't know where it's going, but trust me, it's not intentional,'" Buck said. "He said, 'OK, thank you.'"
- Atlanta OF Jason Heyward and C Brian McCann were rested.
- LHP Mike Minor (9-5, 2.98 ERA) starts against St. Louis ace Adam Wainwright (13-5, 2.44) when the Braves begin a seven-game homestand Friday night.
- Justin Turner started at SS for the Mets, giving Omar Quintanilla a much-needed breather.
- Collins said Wright checked out fine after getting hit in the back of the neck and head Wednesday night with the broken barrel of his own bat on a double-play grounder.