The AL Central-leading White Sox, who also received cash in the deal, have been looking for a third baseman because Brent Morel has been plagued by back problems.
The Red Sox will absorb all but $2 million of the $7.8 million still owed to Youkilis, sources told ESPN The Magazine's Buster Olney.
"There is no way we are not a better team with Kevin Youkilis," White Sox captain Paul Konerko said. "He is just too good of a player and has been through all the wars and is still relatively a young guy. We just have to keep him on the field. If that is the case, it could be one of the bigger steals of the season."
Will Middlebrooks' emergence in Boston made Youkilis expendable after a successful 8½-year run with the Red Sox. The versatile All-Star, who can play both corner infield spots, is a career .287 hitter with 133 homers and 563 RBIs.
"I think we were trying to find a solution that worked for everyone," Red Sox general manager Ben Cherington said. "Kevin's been an everyday player since he's been here, and with the way Middlebrooks has been playing, Middlebrooks needs to be in the lineup. That's pretty clear."
Middlebrooks is hitting .326, and his sacrifice fly in a 9-4 win over the Atlanta Braves on Sunday gave him 34 RBIs in his first 41 games, the most by an American League player in his first 41 games since Wally Joyner had 39 in 1986.
Middlebrooks credited Youkilis for teaching him the right way to play, posting this message on Twitter on Sunday night: "It was truely an honor playing with and learning from Youk... He's the definition of a professional. Played the game right."
Youkilis has been hampered by a variety of injuries the past 2½ seasons. He missed three weeks earlier this season with back discomfort and was limited to 120 games in 2011 and 102 in '10.
"We were given a good bill of health on him," White Sox GM Kenny Williams said. "He said he hasn't felt this good physically for a long time. He said he is very excited to join our club and he has a little bit of edge to him, which I like. I can't tell you exactly what he said, but he wants to come in and prove some people wrong."
Youkilis, who had been held out of the lineup for three straight days, started at third base and hit sixth Sunday against the Braves. When he left the game for a pinch runner after hitting a triple in the bottom of the seventh inning, he received a long standing ovation, blew a kiss to the sellout crowd at Fenway Park and hugged his teammates.
At the strong urging of Red Sox manager Bobby Valentine, with whom Youkilis has had some public disagreements, Youkilis came out for a curtain call. Youkilis also received a standing ovation when he came to bat in the bottom of the second inning.
Prior to the bottom of the seventh, Cherington told Valentine in the tunnel from the dugout to the clubhouse that there was a "situation pending." As Youkilis stepped to the on-deck area, Valentine informed the players in the dugout of that situation.
Youkilis finished the game 2-for-4 and was 6-for-14 in his last four games with the Red Sox. He was a member of the 2004 and '07 championship teams, a three-time All-Star and a Gold Glover at first base.
His departure leaves David Ortiz as the only member of the 2004 championship team still with the Red Sox.
The impact that Youkilis had on the organization goes beyond the numbers and accolades, as evidenced by the reaction the fans gave him Sunday and the way his teammates talked about him in a clubhouse now void of one of its leaders.
"He pushes me every day, and I want to go out and play hard every day just like he does," said Dustin Pedroia, who was the first player after pinch runner Nick Punto to greet Youkilis when he left the game in the seventh. "You know, he's always out there doing his best to try to help us win. I appreciate him so much for that."
Punto said his moment with Youkilis was not planned, but a natural occurrence when the emotion started to spill all around Fenway.
"I know how much blood, sweat and tears he has poured into this organization," said Punto, who has been friends with Youkilis for years. "That just happened. It was a pretty cool moment for me, too."
The moment brought Red Sox players pouring from the dugout to greet Youkilis before he hit the top step.
"It brought a tear to my eye," Cody Ross said. "To see him run off and tip his hat and have tears in his eyes. It was just a special time. I know how much he means to this city. Two World Series here. Played his heart and soul out every day. Just a great teammate. I'm going to miss him."
After his curtain call, Youkilis waved once more to the crowd before disappearing down the tunnel to the clubhouse for the last time as a member of the Red Sox.
I said, 'OK, we'll do it the right way,'" Valentine said of his reaction to Cherington's words. "Someone was looking down because that was the perfect way to end it."
Stewart, 25, was scratched from his start for Triple-A Charlotte. The right-hander went 1-2 with a 6.00 ERA in 18 games -- one start -- for the White Sox before a demotion within the last week. A former third-round pick by Cincinnati, he was shipped to Toronto in 2009, and then to Chicago last year in the deal that sent Edwin Jackson to the Blue Jays, who then shipped Jackson to St. Louis.
In 31 games and 12 starts in the majors, Stewart is 3-8 with a 5.92 ERA.
"We believe he can develop into a good major league starter," Cherington said. "We want to get him back in that role. He's a big, physical, strong kid with three solid pitches. Throws strikes, has had a good minor league track record. He's a guy that looks like a major league starter but just needs a little more time at Triple A to fine-tune things. We're excited, and he'll be a big part of our pitching depth going forward."
Lillibridge, 28, is hitting just .175 with two home runs. However, he had 13 homers last season and does have some speed; he has stolen seven bases in nine attempts in 2012. Lillibridge has played every position except catcher in his career.
"It's part of the business," Lillibridge said of the trade. "You never expect that's going to be you in a trade like that. I'm excited. At the same time I love playing here. I enjoyed it so much, the guys here and the fans. I'm going to miss this place a lot. It's dear. I've been here a long time. I'm excited, though, to see personally where my career will go and to help the Red Sox. But it's tough. It's always tough."
Tony Lee is a regular contributor to ESPNBoston.com. Information from The Associated Press, ESPN The Magazine's Buster Olney and ESPNChicago.com's Bruce Levine was used in this report.