Encarnacion's two-run single in the third inning put the Blue Jays ahead 4-0 and he added a three-run homer in the seventh as Toronto breezed to a win in the opener of a four-game, home-and-home interleague series.
Colby Rasmus and J.P Arencibia each added a two-run clout in the victory.
Buerhle (2-3) allowed one run on five hits over six innings, snapping a seven-start winless streak. The veteran left-hander walked two and struck out six.
Braves starter Tim Hudson (4-4) was roughed up for six runs on eight hits over six full frames.
Evan Gattis went 3-for-4 with a two-run homer for National League East-leading Atlanta.