Encarnacion hit a three-run drive into the second deck in left in a five-run fourth inning as the Blue Jays avoided a three-game sweep. Lind hit a two-run shot to right in the first.
Hernandez (13-8) allowed a season-high seven runs and 10 hits in four innings, struck out four and walked one. He has a 9.00 in his last three outings, losing three consecutive starts for the first time since Sept. 12-24 last year.
Hernandez is 2-3 since throwing the major leagues' 23rd perfect game against Tampa Bay on Aug. 15.
Henderson Alvarez (9-12) allowed three runs in seven innings to beat his childhood idol. Both men were born in Valencia, Venezuela.
Alvarez, who walked three and struck out two, has won back-to-back starts for the first time since July 22-28.
Brad Lincoln and Aaron Loup each worked one inning of relief as Toronto avoided a sixth straight defeat to Seattle.
Trailing 2-0 on Lind's homer, the Mariners tied it in the second on Carlos Peguro's two-run double over left fielder Rajai Davis.
Brett Lawrie's two-run single put the Blue Jays ahead in the fourth, Colby Rasmus walked and Encarnacion followed with a drive to left. He moved one behind Texas slugger Josh Hamilton, who leads the major leagues with 41 homers.
Jeff Mathis hit an RBI single off Carter Capps in the fifth for an 8-2 lead, and Dustin Ackley hit a solo homer off Alvarez in the seventh.
Mathis matched a career high with the third fourth-hit game of his big league career, his second this season.
NOTES: When Encarnacion's bat shattered on his groundout in the first inning, the barrel flew into the Blue Jays dugout and struck pitching coach Bruce Walton on a forearm. Walton, who sustained a bruise, was taken for precautionary X-rays. Bullpen coach Pete Walker replaced Walton on Toronto's bench. ... Davis was nearly thrown out after making a big turn around first on his infield single in the third and was later thrown out at third after going too far round the bag on Mathis' bunt single. ... Blue Jays RHP Chad Jenkins is expected to head to Instructional League next week to get work as a starter, allowing him to be stretched out enough for a major league start before the end of the season. ... Seattle INF Carlos Triunfel doubled in the ninth, his first career hit.