Wheeler was displeased with his results. He said he achieved one of his three strikeouts on a slider.
"I can't remember the others," he said. "I'd like to forget what I did."
Wheeler walked one and allowed three hits. He was likely reluctant to work the Braves as he might have if the teams didn't play each other so often in Spring Training and early in the regular season.
The Mets' first road trip -- April 8-10 -- is to Atlanta.
Wheeler's counterpart, Kris Medlen, the Braves' likely Opening Day starter, removed himself from the game in the fourth inning after grabbing his right arm. Medlen had undergone Tommy John surgery in 2010 and missed most of the 2011 season. But the initial diagnosis was a right forearm strain.
Medlen pitched 3 2/3 innings, allowing a run on three hits. He walked none and struck out two.
The Mets had scored against Medlen in the second inning on a single by Curtis Granderson, a groundout by Travis d'Arnaud that moved Granderson to second, and singles by Matt Clark and Brandon Allen.
A double by Ramiro Pena drove in Mark Hamilton with the tying run for the Braves against Josh Edgin in the seventh.
Up next: Brandon Beachy will make his third start of the Grapefruit League season when the Braves travel to play the Phillies in Clearwater on Monday at 1:05 p.m. ET (watch on MLB.TV). While pitching at this same location last week, Beachy produced three scoreless innings and confirmed he felt more comfortable than he had while allowing two runs in his spring debut. Freddie Freeman, Jason Heyward and Justin Upton are all expected to be in Atlanta's lineup. This game will give manager Fredi Gonzalez his first chance to test the expanded replay system.
Marty Noble is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.