But he regrouped quickly, received a clutch two-run triple from shortstop Josh Wilson in the eighth inning, and kept alive his chances of becoming the Mariners' second Cy Young Award winner, as Seattle held on for a 5-4 victory over the Blue Jays before 15,306 at Rogers Centre.
With starts scheduled against the Athletics and Rangers during the final week of the regular season, Hernandez appears to be in a neck-and-neck race with Royals right-hander Zack Greinke for the American League Cy Young Award.
"I would vote for Felix, without a doubt," said manager Don Wakamatsu after the Mariners notched their 80th win of the season. "I don't know if anyone has meant as much to his club as he has with this one."
Of Hernandez's 17 wins this season, 14 of them -- including Thursday night -- have come after the Mariners lost their previous game.
"The impact he's had on this club, especially after last year, is remarkable," Wakamatsu said.
Hernandez, 17-5, surrendered four runs (three earned) in the series opener to the Jays, but it was a marked improvement over the last time he faced them. They tattooed him for 11 hits and seven earned runs on July 27 at Safeco Field.
It was his worst outing of the season.
The rematch wasn't Hernandez's best overall, but he struck out a season-high 11 batters, surpassing the 200-strikeout mark for the first time in his career.
"I struck out on seven pitches in my first two at-bats," Jays center fielder Vernon Wells said. "His stuff was unbelievable tonight. He left a lot of guys shaking their heads, just trying to figure out what to do just to put the ball in play. I think the only chance I had was to hopefully hit something offspeed he left up."
He got that pitch in the sixth inning and sent it over the left-field fence for a game-tying three-run homer.
The get-even jolt came on the first pitch of the at-bat and followed on the heels of an error by third baseman Adrian Beltre and an ensuing single, only the second hit of the game off Hernandez.
"The error didn't bother me," Hernandez said. "That's part of the game. I made two mistakes."
Wilson's two-run triple in the eighth inning proved to be the game-winner.
"I was just looking to hit a good pitch," he said. "I was finally feeling like I was getting a little rhythm back and not thinking as much about what my hands were doing, what my feet were doing.
"I was focused in on what kind of pitch I thought [left-hander Jesse Carlson] was going to throw me and look for it in a good spot. I was pretty relaxed and the second-pitch slider was over the plate for me. I put a good swing on it."
The drive into the right-center gap scored Beltre from second and Bill Hall from first.
Though the Jays retaliated with a run in the bottom of the eighth, right-handed closer David Aardsma overcame a leadoff walk in the bottom of the ninth to nail down his 36th save of the season.
Nailing down a Cy Young Award, and joining Randy Johnson as the only Seattle pitchers to be so honored, isn't something Hernandez is giving a lot of his attention.
"If it happens, it happens," he said, "and if I had a vote, I'd vote for Greinke. He's had a great season."
But has the Royals ace had a better season?
That's for the voters to decide and it could be close.
Here are some comparisons:
Hernandez has a 10-3 record against teams with a winning record this season and Greinke is 6-4.
Hernandez has a 2.15 ERA (35 earned runs in 146 1/3 innings) against teams with a winning record while Greinke has a 0.57 ERA (six earned runs in 95 innings).
Hernandez is 5-1 against probable playoff teams and Greinke is 4-2.
Hernandez has pitched at least seven innings 22 times, three more than Greinke.
Hernandez faced the Dodgers, Giants, Padres and Diamondbacks in Interleague Play. Greinke faced the Astros, Pirates and Diamondbacks.
Hernandez's longest winning streak was seven games, one longer than Greinke's hottest streak.
Seattle's ace has 10 no-decisions, two more than Greinke.
The Mariners scored 21 runs in the five games Hernandez lost, and the Royals scored 15 runs in the eight games their ace lost.
Hernandez plays for a team that averages 3.95 runs per game (last in the AL) while Greinke's team scores an average of 4.24 runs per game.
Asked about the best young pitchers in the AL, Wells said, "The discussion has to start with [Hernandez]. When he's on like he was tonight, it is fun to watch. It's not fun to be in the box facing it, but it's amazing the kind of stuff he has at such a young age."
"It was a great win, especially after getting in at 5 a.m. [from Florida]," Wilson said. "You always wonder how guys are going to come out and play and I thought we played tough the whole game.
"It's always tough, but I think you try to remind yourself of those days back in Class-A when that was typical. You just remember when you had to do it all the time."
Jim Street is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.