After the White Sox fifth straight win, Thome said he felt fine and would be ready to go Friday for the series opener at home against the American League East leaders from Tampa Bay.
Both Thome and Ozzie Guillen talked about the problem being more in the lower abdominal area, with the White Sox manager describing it as "a little stomach" thing.
"He's good," said Guillen of Thome. "Hopefully he'll be better for the next day."
Thome was replaced by DeWayne Wise. Ken Griffey Jr. moved from right field to designated hitter and moved up two places into the cleanup spot, with Nick Swisher switching to right and Wise taking over in center field.
Guillen already had decided to give Jermaine Dye the day off prior to Thome's removal. Although Thome has just five hits in his last 29 at-bats, he has been going strong in his last 33 games with a .300 average, 10 home runs, 29 RBIs and 24 walks.
Thome launched career home run No. 532 leading off the fifth inning of Tuesday's 5-0 whitewash of the Mariners. Thome's 26th home run this season moved him within two of Jimmie Foxx for 15th place on the all-time list and within four of Mickey Mantle, a player often mentioned by Thome's father, Chuck, as one of the game's greats.
"When you mention Mantle, he really is an all-time great," said Thome after Tuesday's victory. "All of those guys are. To be on that list, we've talked about it. It's very surreal and humbling.
"On the other end, it's really cool to be talked about in that group," added Thome with a smile. "You appreciate the game itself and what those guys have done in the game. We have a teammate on that list, too. It's really cool to do that for sure."
Wise eventually was replaced by Brian Anderson in center field to start the fifth inning, after Wise made a diving catch on Bryan LaHair's line drive to center to end the top of the fourth. Wise left with a strained left adductor, suffered during the spectacular catch, an injury that sounded a bit more serious than Thome's one-day absence.
"I don't know yet," said Guillen, when asked about his fleet-footed reserve outfielder. "It doesn't sound too good."
Scott Merkin is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.