But one day after Yankees rookie Mark Melancon fired one heater over Pedroia's head and buried another in the second baseman's left shoulder during New York's 13-6 victory, Yankees manager Joe Girardi reiterated that the eighth-inning plunking had been unintentional.
"Come on, we're not trying to ruin someone's career," Girardi said on Friday. "We talk about pitching inside effectively and we tell them to pitch down, waist [and] below. But these are human beings. These aren't robots that have Nintendo controllers in their pocket and can direct the baseball wherever they want it to go.
"Some pitchers are much more capable of throwing the ball exactly where they want to on a consistent basis. Those guys are called Hall of Famers."
Melancon, 24, was beginning the eighth inning and soaking up work as the fourth Yankees pitcher, protecting a 13-4 lead when he hit Pedroia.
"I was trying to elevate a fastball on the first one," Melancon said. "I elevated it, but it got inside as well. The second one, I was just coming in, and, obviously, not trying to come that far in."
After being hit, Pedroia walked down to first base trailed by Yankees catcher Jorge Posada, appearing to yell at Melancon. Red Sox manager Terry Francona also came out of the dugout to voice his displeasure.
"It was kind of surprising, obviously," Pedroia said after the game. "It goes over your head, it's really nothing to mess around with. I don't know. I don't know why they'd be throwing at me if they were. Especially in that situation, it's a blowout. That's fine."
Posada said after the game that it had been "just a pitch that got away." Melancon said that there was no reason to hit Pedroia in that game situation, a point that Girardi also made.
"Obviously, I didn't want him to hit Pedroia," Girardi said. "You didn't want to give them a free baserunner. You don't want to start something. We weren't happy that we hit them, but it happens in this game. You see it a lot of times with young kids."
Melancon faced Pedroia, an Arizona State product, while pitching at the University of Arizona, but said there was no bad blood that he knew of. The fact that Pedroia reacted the way he did, however, was not completely surprising to Melancon.
"Of course, when you get hit, I'm sure it hurts," Melancon said. "But if he thought there was any intention of me throwing at him, he's wrong. There's no intention by me to hit him. I mean, we're up [nine] runs at the time. I'm just trying to throw strikes and get outs."
Melancon said that he has been taken aback at how hot the discussion seems to have grown.
"I'm a little bit surprised, just because it was totally on accident," Melancon said. "I guess it's Boston-Yankees. That's the only reason why it is a big deal."
Girardi said that he did not know if there might be any retaliation from the Red Sox on Friday, with Josh Beckett starting opposite New York's A.J. Burnett.
"I know clubs feel that they have to protect their players," Girardi said. "I can 100 percent say that that was not on purpose. The ball got away from a young kid. You hope that this doesn't lead to something that [gets] things get out of hand. You play the game and you don't worry about it. There's not a whole lot as a manager that I can do about it."
Melancon hurled 1 1/3 scoreless innings to help preserve New York's first victory in nine games against Boston this year. Given a similar circumstance, Melancon said he wouldn't entertain not pitching inside so much with a huge lead.
"I'm still trying to earn a spot here," Melancon said.
Bryan Hoch is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.