With one out in the ninth inning and Chamberlain in the middle of his second inning of work, the 21-year-old Yankees reliever threw consecutive fastballs high and inside to Youkilis -- the second of which sent him diving to the ground and prompted an immediate ejection from home-plate umpire Angel Hernandez.
Chamberlain threw up his hands in a mixture of confusion and disgust before leaving the game.
"There's no chance I'm trying to do that," Chamberlain said of his intent. "I definitely don't want to send that message, because that's not who I am."
Youkilis anticipated Chamberlain's reaction, and rebuffed it in advance.
"Two balls going over somebody's head at 98 mph, I don't know," Youkilis said. "I didn't see any other pitches going that far out of the strike zone. Those balls were pretty close to the head."
"That's the second time," Youkilis continued, referring to a similar situation that occurred on June 1. "Scott Proctor hit me in the head. Coincidence? I don't know. It doesn't look good. When two balls go at your head and the guy has a zero ERA and is around the strike zone pretty good, any man is going to think there's intent to hit him in the head."
Youkilis first lost his temper in the seventh inning on Thursday, when he was ruled out for running out of the baseline between second and third. After J.D. Drew hit a grounder to Yankees third baseman Alex Rodriguez, Youkilis made a dash toward third, while Rodriguez attempted to tag him en route. The tag missed, and second-base umpire Derryl Cousins originally ruled Youkilis safe, before umpires gathered and reversed the call based on third-base umpire Mark Carlson's perspective.
Youkilis, noticeably irked, crossed paths with Francona on his way back to the dugout. The Red Sox manager argued with umpires for several moments before getting ejected by Cousins.
So when Chamberlain twice threw near Youkilis' head during the first baseman's next at-bat, the umpiring crew wasn't about to take a chance.
"There is more than a little bit of history between these clubs," Cousins said. "Those were two pretty nasty pitches the young man threw. Up here, you need to be a little better throwing strikes, and we just had to put a lid on it before there was a problem."
Much of Youkilis' anger stemmed from the fact that Chamberlain seemed to have pinpoint control throughout his scoreless eighth inning -- and throughout his young career. He remains unscored upon in 11 1/3 innings this season, and has walked only three batters during that stretch. Over 88 1/3 Minor League innings almost exclusively as a starter, Chamberlain walked 27 batters.
Yankees manager Joe Torre, however, saw the situation differently. He said that with a game -- and a series sweep -- on the line, putting runners on base was the last of his desires.
"To me, that was strictly the safest thing to do, instead of the thing that made sense," Torre said of the ejection. "There certainly wasn't a message. You're certainly not going to send a 21-year-old kid out there with limited experience to send a message. That's absolutely ridiculous."
The Yankees and Red Sox have seen their rivalry take a tumultuous turn since the turn of the century, highlighted by two recent memorable fracases. In 2003, benches cleared as then-Sox starter Pedro Martinez threw then-Yankees bench coach Don Zimmer to the ground at Fenway Park. Then, the following year, Rodriguez and Red Sox catcher Jason Varitek sparked a benches-clearing incident after Sox starter Bronson Arroyo hit A-Rod with a pitch.
Yet tempers have cooled since those exchanges, and no major on-field episodes have surfaced since the Red Sox won the World Series in 2004. And because of that seemingly newfound peace, Torre expressed even more displeasure when accusations flew about his newest reliever.
"It makes no sense, and unfortunately in a lot of situations, the umpires do not apply common sense," Torre said. "I've seen it too many times, and something has to change."
Varitek had no comment, and pitcher Curt Schilling said simply, "I don't know what to think."
Yet Chamberlain did, and wasn't shy to voice his opinion -- perhaps the least contentious opinion of all.
"I'm new to this whole thing, and the last thing I want to do is send a bad message," said Chamberlain, who was in line for a save before exiting. "I have the utmost respect for Youkilis. He plays the game right."
Chamberlain noted that he's still trying to become acclimated to the Major Leagues, and due to the way he pitches -- routinely hitting 98 and 99 mph on the radar gun -- mistakes are bound to happen.
His pitches to Youkilis were 97 and 98 mph, respectively, and gave him plenty of regret -- little of which centered around their implication.
"The biggest thing was I let my team down," Chamberlain said. "I feel worse about that. There was nothing behind it. I'm more mad at myself."