He felt playing on the artificial turf in Toronto and Tampa Bay contributed to the discomfort. Will he play Thursday?
"We'll see how I feel tomorrow, and go from there," Fukudome said.
Cubs manager Lou Piniella doesn't expect Fukudome to play in the series finale.
"This is the first time that I was aware of [the injury]," Piniella said. "He went out and ran before the ballgame, and he ran about 75 to 80 percent. That's about as good as he could do, and he felt it. With all the injuries we have here, there's no sense taking any chances with that. Let's get him well, and then we'll get him back in the lineup."
Fukudome, who is hitting .373 at Wrigley Field, was scheduled to lead off.
Before the game, Piniella was asked if Tuesday's loss was a result of a letdown after the Interleague series against the crosstown White Sox.
"No," Piniella said. "What I'm concerned about are all these injuries we're starting to encounter. There's no letdown. We played a good ballgame last night, and we got beat. We had chances. The team fought. We weren't flat.
"We had that one inning where we gave them some runs. That's not our problem. Our problem is we're starting to get a little thin."
Fukudome has reached base safely in 15 straight games dating to June 7, posting a .409 on-base percentage.
Eric Patterson was inserted into the leadoff spot on Wednesday.
Carrie Muskat is a reporter for MLB.com. Nick Zaccardi contributed to this report. This story was not subject to the approval of Major League Baseball or its clubs.