"They only hit two balls hard against him. They both went over the fence," said Red Sox manager Bobby Valentine. "It was a pretty good outing."
Cook went 6 1/3 innings, allowing four hits and five runs, three of which were earned.
"They were pitches that came back over the middle of the plate. If I had two pitches to take back the whole game, those would be the only two," said Cook. "Other than that, I was in a pretty good rhythm putting the ball where I wanted to. Just those two bad pitches, they made me pay for them tonight."
If the Red Sox had been swinging the bats better, perhaps they would have won in spite of the two misfires by Cook.
Once again, the Red Sox weren't able to add on offensively and it cost them.
"We need to find a way to score more runs," said Red Sox second baseman Dustin Pedroia. "I need to do a better job. A lot of guys need to do a better job. We will. We will do that."
After the Red Sox honored their former catcher Jason Varitek before the game, successor Jarrod Saltalamacchia stepped up with a three-run homer to right to break a scoreless tie in the bottom of the second.
For Saltalamacchia, it ended an 0-for-14 drought, and it was also his first start since Tuesday.
"Men on second and third, no outs, you're trying to get the ball in the air, trying to score those guys," Saltalmacchia said. "He left a slider up that I was able to do some damage with and that's it."
Though Saltalamacchia's blast didn't contribute to a win, it could be important in the big picture. His bat is important, particularly at a time when David Ortiz is out of the mix.
"Perfect," Valentine said. "Just what the doctor ordered for Salty, and it came with two strikes and he laid off a tough pitch down in the zone. It was good."
The Jays got one of those runs back against Cook in the top of the third. With the bases loaded and one out, Brett Lawrie lifted a sacrifice fly to right.
While Toronto starter Carlos Villanueuva got into a groove, Cook was mostly dominant over the first five innings. He also retired the first two batters in the sixth.
But after a two-out walk to Colby Rasmus, Encarnacion silenced the Fenway faithful by hitting a mammoth two-run homer that soared into the parking lot behind the Monster.
"It was just one of those things," said Cook. "A walk and a home run -- you can't walk people before you give up home runs. Solo home runs don't hurt you that bad, but that at-bat, I just kind of lost command a little bit and was trying to get back into it with Encarnacion coming up next, and just left one that leaked back over it a little bit. I just missed my location."
Unfortunately for the Red Sox, there was more of where that came from in the seventh, as Arencibia led off by depositing a misplaced sinker by Cook over the Monster. That gave the Blue Jays their first lead of the night.
"Cook was that good in the first five," said Blue Jays manager John Farrell. "Very good sinker, threw a lot of strikes. Any ball we put in play seemingly was on the ground with a relatively easy-made defensive play. But he gets a ball up on the plate, he hits it out of the ballpark and whether it was a combination of us coming to life or maybe a little less sink or power to his sinker, we were able to string some quality at-bats together."
Two batters later, Yunel Escobar reached on an error by third baseman Will Middlebrooks, leading to more bad things for the Red Sox. Franklin Morales came on in relief of Cook and struck out Travis Snider. But the lefty walked Rajai Davis, and Valentine then called on righty Matt Albers. The Blue Jays executed a double steal with Escobar and Davis. With two runners in scoring position, Lawrie drove them home with a two-run single through the hole in left.
"Especially in our division, teams keep coming after you and coming after you," said Pedroia. "We need to try to separate ourselves. There's nothing wrong with getting a five-, six-run lead. Other than that White Sox game where we scored a bunch, it's been close and we need to make sure we have better at-bats and try to pull away. It makes it easier on our pitching staff."