Encarnacion finished 2-for-4 for the Blue Jays, who swept the Brewers in this short two-game set. Jose Bautista also homered for Toronto, which finished with 11 hits and overcame a 3-for-13 effort with runners in scoring position.
Ryan Braun drove in a pair of runs to lead the Brewers, who have dropped three straight after winning four in a row.
With two outs and runners on the first and second, Encarnacion drove a 3-1 pitch from Brandon Kintzler into the second deck in left field to give Toronto the win.
Milwaukee reliever Will Smith (1-1), who was responsible for the runner on second, suffered the loss.
Toronto reliever Casey Janssen (3-0) worked a perfect top of the ninth and got the win.
Milwaukee took a 4-1 lead against Toronto starter J.A. Happ in the third when Braun tripled home a pair of runs and scored on a Lucroy sac fly.
Braun ended 2-for-4, extending his hitting streak to eight games.
Reyes went 2-for-5.
Happ recovered after the early woes, retiring 13 straight until a one-out bunt base hit in the seventh by Martin Maldonado. However, Happ responded to retire the next two batters to get out of the inning unscathed to end his afternoon.
Happ was charged with four runs on six hits, striking out four without a walk, in seven innings.
Milwaukee starter Wily Peralta also received a no-decision, yielding four runs on nine hits in six-plus frames. He struck out four and walked three.