Lilly will go for tests Friday at Northwestern Hospital for an arthrogram to determine the extent of the injury or soreness.
In addition, Lilly has been suffering with a left knee problem the past three weeks.
The Cubs open a three-game series against the Cincinnati Reds on Friday.
Kevin Hart will fill in for Lilly on Saturday, according to a team source.
Lilly, Chicago's only All-Star this season, is 9-7 with a 3.59 ERA. He is coming off his worst start of the season, having allowed nine runs in four innings in Monday's 10-1 loss at Philadelphia.
Bruce Levine covers baseball for ESPNChicago.com. Information from The Associated Press was used in this report.