The right-handed Medlen left the game in the fifth inning after hurting the ulnar collateral ligament in his pitching elbow. He will have an MRI exam on Thursday.
Chipper Jones and McCann hit back-to-back homers off Mike Pelfrey (10-6) in the third inning. McCann's line-drive shot into the right-field seats gave the Braves a 3-2 lead.
Melky Cabrera added a homer off Raul Valdes in the Atlanta eighth. Jones had three hits and drove in two runs.
The NL East-leading Braves won two of three from the Mets after losing three straight series.
The Mets, who won Tuesday night, have not won consecutive games since June 22-23. They have not won a road series against an NL opponent this season.
The loss of Medlen would be a blow to the Braves' hopes of holding off Philadelphia in the NL East. He's in his second year and has been one of Atlanta's most effective starters after taking over the No. 5 spot in the rotation from Kenshin Kawakami.
The Braves are 13-1 in Medlen's 14 starts. He gave up four hits and two runs in 4 1-3 innings.
McCann had run-scoring doubles in the first and fifth innings. The All-Star catcher has six homers and 23 RBIs since July 3.
The Braves scored four unearned runs on four New York errors, including two errant throws by shortstop Jose Reyes. Three errors came when the Braves scored two unearned runs off Hisanori Takahashi in the sixth.
Reyes and third baseman David Wright had throwing errors in the sixth. First baseman Ike Davis had a fielding error.
Wright's error came after fielding a bases-loaded grounder by Jones. Reliever Mike Dunn, who reached on Reyes' second error, scored on Jones' grounder. Wright's wild throw to second allowed Omar Infante, who reached on a single, to score from second.
Dunn (1-0) gave up two walks in 1 2-3 scoreless innings in his first major league win.
Medlen left his last start on Friday in Cincinnati after he was hit on the inside of his right forearm by a pitch from Johnny Cueto.
Medlen showed no sign of discomfort against the Mets before throwing an outside pitch to Reyes with one out in the fifth. Medlen took a couple of hops off the mound, and manager Bobby Cox quickly came out of the dugout to the mound. Medlen appeared to try to flex his arm before leaving the game.
New York's Luis Castillo had two hits, including a run-scoring single in the second. Reyes doubled and scored on a groundout by Carlos Beltran in the third.
Pelfrey gave up eight hits and five runs, three earned, in 4 2-3 innings while losing for the fourth straight time.
NOTES: The Mets' four errors are their high since their five against the Dodgers on May 18, 2009. Their last three-error inning came on June 26, 2009, against the Yankees. ... Braves LHP Eric O'Flaherty, recovering from mononucleosis, threw on the side and is expected to throw in the bullpen on Thursday. ... The Mets are 0-6 in decisive third games of series on the road, and 4-11 overall.