"I just lifted, worked out," Youkilis said before Tuesday's game. "There's nothing."
Francona made the decision after Monday's 7-3 loss.
"I really don't want to sit anyone," he said. "It's a good night to do it with Youk."
Coco Crisp also sat for the third straight night to rest his left oblique. The Boston center fielder had three straight multihit games leading up to the injury and had hit safely eight times in 20 at-bats.
Francona inserted Crisp as a defensive replacement on Sunday night, but Crisp didn't bat. Francona had considered playing Crisp on Monday and Tuesday, but decided against it both times on trainers' advice.
"Problem is, every player tells you they're fine," Francona said. "And then they take one swing or they do one move and then they miss six weeks and it doesn't make sense."
A Fenway salute: When Daisuke Matsuzaka hit Alex Rodriguez with his first pitch to the Yankees star on Sunday night, the Fenway faithful stood and roared. Matsuzaka grimaced and tipped his cap quickly as a way of apologizing. Matsuzaka told the Japanese media after the game that he was torn about whether to make the move, which is a common convention in Japanese baseball.
In the third inning, Matsuzaka plunked Derek Jeter with a fastball. He did not tip his cap.
"He's probably used to doing it, he probably did it, then he thought, "Well, you know, maybe we don't do it here,'" said Francona on Tuesday.
Francona refused to go further, saying he had not seen Matsuzaka tip his cap but that he was not bothered by the gesture.
"His etiquette is fine," Francona said. "He's a nice kid."
Cora values: When Francona slipped down the tunnel during a break in Friday night's game against the Yankees, he saw utility man Alex Cora swinging on a tee that was set bizarrely high.
The Red Sox were headed for a certain Mariano Rivera save situation, and Cora was practicing swinging at high pitches and jam shots, a Rivera specialty.
"I was kind of laughing," Francona said. "I wasn't laughing when he drove [the winning run] in."
Pinch-hitting with one out in the eighth and Crisp representing the winning run on third, Cora looped a high, 93-mph fastball over the drawn-in infield and Jeter. The hit drew comparisons to another famous flare against Rivera in one of the Yankees closer's less finer moments.
In his blog, Curt Schilling called it "a carbon copy of [Alex Gonzalez's] floater in the ninth inning of [Game Seven] of the 2001 World Series." Schilling was co-MVP of that World Series for the Arizona Diamondbacks, which beat Rivera and the Yankees that year.
Clement update: Former Red Sox rotation regular Matt Clement continues to make progress in Fort Myers, Fla., as he rehabs his right shoulder.
Francona said he texted Clement "probably three or four days ago." The right-hander had arthroscopic surgery on his right labrum and rotator cuff in September and is now throwing long toss at 105 feet.
But Francona said Clement has "a ways to go."
"He's at a point where there's a lot of repetition and it's boring, but he's got to do it," Francona said.
On deck: Schilling will bring a 3.81 ERA into Baltimore on Wednesday sat 7:05 p.m. ET as he seeks his third win against starting pitcher Daniel Cabrera and the Baltimore Orioles. In his career against the Orioles, Schilling is 5-4 with a 4.00 ERA, which is a much higher 5.28 ERA on the road at Camden Yards.