After learning that the coaches and support staff were not going to receive a stipend for the trip to Japan, the Sox threatened to boycott both the game and the trip before a resolution was reached.
"We've come to a good negotiation on the coaches," said Youkilis, whose three-run home run in the third inning accounted for all the Sox's runs in their 4-3 loss to the Jays.
"First and foremost, we want to thank all our players. They did a lot of good, not just for the coaches, but all around baseball. There's a reason why we have one of the strongest unions in all of the world. It's because we have guys who are willing to fight and willing to basically put their best interests on the back burner.
"The coaches are a huge part of our success. They have been for many years. This was something that, as players, we felt really strong about. We want to apologize to the fans out there that had to sit around a little longer, and to the fans who might have been upset at first, but this is something that we felt strongly about and still feel strongly about."
The plans for the trip stemmed from a conference call shortly after the 2007 season ended that included players and baseball officials.
"The conference call was tough in itself," Youkilis said. "There were probably six or seven players on it. It's very difficult. I think, as a lot of people know in the business world, conference calls are not the easiest way [to conduct business]. You have voices here and there and you don't know who's talking. But we definitely know what we were told: That there was going to be a lot of added stuff just to get us to go over there. With what we bring as a team, and with some of our players [as] celebrities in Japan, we bring a lot going over to Japan.
"We have a lot of players on our team who are smart and understand the business side. There's a lot of stuff that goes on behind closed doors. I can't really blame any one person for the misunderstandings that have happened. I think going forward, when you have these conference calls, you need to put things in writing. That will be addressed at the players' union meetings now. We have to make sure we're on the same page. There's stuff we found out today. So now it's a learning process. We're going to move forward and have a lot of fun over there in Japan."
While this is not the first time teams have made these kinds of trips -- the Yankees and Rays played in Japan in 2004, for example -- it is the first time an issue has existed in compensation for coaches and support staff.
"I couldn't answer why it became an issue," Youkilis said. "There were certain things here that I couldn't tell you. I don't understand why it was an issue, but for some reason, it ended up that way. ... So to tell you I know exactly how it came about, it doesn't make sense, because [I don't know]. ... It didn't make sense to us and we didn't understand it. But ... at the end of the day, we resolved it."
Youkilis said the breakdown in the original agreement was attributable to poor communication and could not say whether Major League Baseball or the Major League Baseball Players Association was at fault.
"It's always like that in baseball," Youkilis said. "It's always the sides going back and forth. It's tough. It was definitely a bad communication, and for us to come into a clubhouse and see our coaching staff not getting compensated for putting forth the time and effort -- way more time and effort than the players put in.
"A lot of people don't realize these guys come to the field and are here for sometimes almost 11, 12 hours. They put in a lot of time and effort, and they deserve to be compensated for big trips like this, because trips like this are very tough for trainers and coaches and all the time and effort they have to put in."
After the game, general manager Theo Epstein, on his way to the team bus, was hesitant to discuss the matter.
"It doesn't serve for a quick summary," Epstein said. "But I think you guys kind of know the basics. ... [We were] trying to reach a fair resolution and get this game played and get on the way -- try to make all the parties happy.
"[But] it's always better to play baseball and get on a plane than not play baseball and not get on a plane."
Asked if the team was picking up the tab for the coaches, Epstein replied: "I don't think they want us to get into that too much."
Epstein said he had not been involved in the negotiations before Wednesday.
"[We] have to go back and see what happened in -- what was it? -- November?" said Epstein. "I think only the parties that were on that conference call really know what happened. It just took untill today to get it resolved."
The team bus left City of Palms Park for the airport at 4:45 p.m. ET.
Maureen Mullen is a contributor to MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.