The late scratch comes one night after Youkilis made his return to the Red Sox's lineup. The 2007 American League Gold Glove Award winner missed the final two games of the White Sox series over the weekend with flu-like symptoms.
"It was a quick move tonight," manager Terry Francona said. "Youkilis was down in the cage just before the anthem and his back was tightening up."
While it will be a decision made Wednesday morning before the 1:35 ET matchup with Baltimore, it is uncertain whether Youkilis will be out of the lineup for the fourth time in five games.
"I guess there's a hope that he would play, but we have a day off the next day," Francona said. "We'll see; I bet you it's 50-50 at best. I don't know if it's the smart thing to do or not."
As a result of the scratch, Jed Lowrie moved from sixth in the batting order to second, Dustin Pedroia replaced Youkilis in the cleanup spot, Jason Varitek moved to sixth and Jeff Bailey, taking Youkilis' spot at first, batted seventh.
Pedroia went 3-for-5 in the cleanup role, driving in five RBIs and scoring once. Bailey, in place of Youkilis at first, went 1-for-3 with two runs scored and two walks.
Youkilis went 0-for-4 on Monday against the Orioles. He's batting .315 with 24 home runs and 94 RBIs in 2008.
Mark Remme is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.