Raul Valdes (2-2) relieved Phillies starter Vance Worley to start the frame, and after getting two quick outs, surrendered a long blast over the center field wall to McCann, which broke a 3-3 tie.
Dan Uggla added a two-run blast for the Braves, who swept the Phillies for the first time in five years in taking the three-game set.
Jair Jurrjens (3-2) recorded the victory, holding the Phils to three runs on six hits over seven innings. The right-hander won for the third time in four starts while surrendering one walk and striking out four.
Kris Medlen tossed a scoreless eighth and Craig Kimbrel fired a 1-2-3 ninth for his MLB-best 25th save.
Jason Pridie went 2-for-3 with a two-run homer and three RBI as Philadelphia fell for the 10th time in 11 games overall.