Youkilis, who charged the mound after being hit in the back by a Rick Porcello pitch in the second inning of Tuesday's game, began his punishment on Wednesday, just hours after the discipline had been handed down.
The star corner infielder is eligible to return on Aug. 18, when the Sox open a three-game series at Toronto. By appealing, Youkilis could have risked missing some more crucial games down the stretch, particularly when Boston hosts the Yankees for a three-game set that starts on Aug. 21.
"I think we just decided to take our medicine and move on," said Red Sox manager Terry Francona. "We seem to be healthy right now. There's always the idea that you could get it reduced. There's also the idea that it could come at a worse time. So take our medicine and do the best we can and move on."
The Red Sox have Mike Lowell, Victor Martinez and Casey Kotchman available in the corner infield. Lowell has been on fire of late, so he figures to get more at-bats while Youkilis is out of the mix.
"Basically I left everything in the hands of Tito and the front office and all them, and whatever they thought was best for the team is good for me," said Youkilis.
Did he think five games was a fair punishment?
"I don't really have an opinion on it," Youkilis said. "It is what it is and you just have to move forward, and hopefully the next couple of days will be quick."
Porcello also got a five-game suspension, and he dropped his appeal as well.
Youkilis had never charged the mound before in his career. But in this case, after the Tigers hit him Monday and again on Tuesday, he felt like there was intent.
"I don't have any regrets, other than like I said before, about the kids -- the kids I work with and my charity and stuff like that," said Youkilis. "[I was] just telling them that it's not the right thing to do. There comes a point in your life when people don't do things in the right manner, then you get kind of fed up with it and you have to do what you have to do in life to protect yourself. I take one ball off the eye or anything like that and my career could be over, and I take a lot of pride in this career."
Youkilis is hitting .311 with 20 homers and 66 RBIs.
MLB also announced that Tigers pitcher Edwin Jackson has been fined for his "aggressive actions" during the incident.
According to the MLB release, Porcello's suspension is for "intentionally throwing pitches" at Boston's Victor Martinez and Youkilis, who was suspended for "charging the mound, throwing his helmet at Porcello and inciting the bench-clearing incident."
Tensions were high early in Tuesday's game when Miguel Cabrera was struck in the left hand by a pitch from first-time Red Sox starter Junichi Tazawa.
Porcello threw a pitch up and in to Martinez in the bottom half of the first, which Martinez made clear he didn't appreciate. Cabrera would leave the game during his second at-bat in the second inning with pain in his left hand.
Porcello hit Youkilis with a pitch in the bottom half of the inning.
Youkilis immediately charged the mound and threw his helmet toward Porcello. Youkilis and Porcello then dragged each other to the ground. From there, both benches and bullpens emptied in a game the Red Sox went on to win, 7-5. Afterward, Porcello denied throwing at the Red Sox's slugger intentionally.
Ian Browne is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.