"We hope Michael's recovery is as quick as possible," read a Chelsea statement.
"We hope he returns to full training soon so that he will then be available for the competition's latter stages."
The Blues submitted their list of players on Friday and could not guarantee that Ballack, who has not played since April, would feature in the majority of the Group B games.
Jose Mourinho's team play Valencia, Schalke and Rosenborg twice before the group stages finishes on 11 December.