Encarnacion's blasts gave him 25 homers for the season while Lind delivered a two-run double in the first inning and a two-run single to cap an eight-run third for the Blue Jays.
Lind finished 4-for-5 while Yunel Escobar chipped in with a two-run homer for Toronto, which evened its three-game series against the Indians.
Aaron Laffey (1-1) collected the victory after yielding four runs on eight hits over five full frames, and Casey Janssen was needed to make his 13th save after the Indians scored five times in the eighth.
Indians starter Ubaldo Jimenez (8-8) was rocked for eight runs on seven hits, lasting only 2 1/3 innings.
Casey Kotchmann also homered with a man aboard in the loss.