Two of the three homers clubbed by Thomas came against Tim Wakefield, which was notable for history purposes. The only other three-homer performance in Thomas' career came against the Red Sox on Sept. 15, 1996, and, on that night, all three homers came against Wakefield.
"Yeah '96, I remember it like it was yesterday," said Wakefield. "There's a reason he's got  homers. You make mistakes to him, and they leave the yard pretty quick."
On a night the Red Sox were trying to bounce back after losing two out of three to the Yankees, they were instead done in by one future Hall of Famer. In the process, Boston's lead in the American League East over New York fell to 3 1/2 games, the smallest it has been since May 1.
"We just have to move on, we have 11 left, there's still some work to do," said Red Sox third baseman Mike Lowell. "We have to play good baseball. We don't want to go into a little rut because one guy pitched well against us."
The Boston bats -- again without Ramirez (strained left oblique) and Kevin Youkilis (right wrist contusion) -- sputtered against Dustin McGowan, who turned in a dominant performance.
In one of the finest games pitched against the Red Sox this season, McGowan went the distance, yielding five hits and a run while walking none and striking out nine.
"We're going to have to fight through this here for a few days," said Francona. "David doesn't feel great. Coco [Crisp's] back acted up on him. We're going to have to fight it a little bit here. That's OK, that's what good teams do. We'll take stock on how guys feel [Tuesday] and go get them."
The Red Sox just hope that A.J. Burnett has a little less than what McGowan had in this one. Red Sox catcher Kevin Cash -- who was with McGowan during his years in the Toronto farm system -- was suitably impressed.
"I think when they first drafted him, everyone kind of knew that he was a special talent," said Cash. "I think he had two arm surgeries and he hasn't been able to avoid injuries. Obviously, he's healthy now. His combination of pitching tonight was as good as I've ever faced. He was tough. When you're throwing 98 miles an hour in the ninth inning, that's pretty impressive."
Just how much has Thomas tormented the Red Sox in his career? His 40 homers against Boston are the most by any active player. Thomas is now tied with Hall of Famers Eddie Mathews and Ernie Banks for 18th on the all-time home run list.
Aside from his encounters with Thomas, it was a nice bounce-back start for Wakefield, who gave up seven hits and four runs over six innings. This was a big improvement over the last couple of outings, when Wakefield did not make it out of the fourth inning.
"I felt like I'd like to have two pitches back, both of them to Frank," said Wakefield. "Unfortunately, it is what it is. McGowan pitched unbelievable tonight. Sometimes you run into situations like that."
The night got off to an unsettling start for Wakefield. Thomas clubbed a two-run homer to left in the bottom of the first to make it 2-0.
"I've had my good days against him," said Thomas. "Today, a couple flattened out. That's all. That happens with knuckleball pitchers sometimes."
The Red Sox were having a tough time getting much established offensively. But they did rally in the fourth, getting a leadoff single from Jacoby Ellsbury and a two-out, RBI double by Lowell to slice the deficit to a run.
But before the Red Sox could get any closer, the Jays spread it back out. Russ Adams got a one-out rally started in the fifth with a walk, and he then stole second. John McDonald's infield single set up runners at the corners. Wakefield nearly got out of the inning with a double play when Vernon Wells hit a grounder back to the box. But Alex Cora's throw to first was not in time, bringing in the run that made it 3-1.
The Big Hurt struck again in the sixth, nailing a solo shot off the foul screen in left, putting Boston in a three-run hole.
"I think Frank squared up two balls and that's all I can remember being hit hard," said Cash. "That's just the way it goes sometimes when you have a knuckleballer out there. He pitched well."
And Thomas capped his magnificent performance by taking Kyle Snyder over the wall in left for a two-run shot, giving him five RBIs on the night.