"A scan this week revealed that Chris is suffering from an inflamed sacroiliac joint. We are monitoring him as a team but unfortunately the injury means he will not be able to take part in the race this weekend," team doctor Alan Farrell said in a statement.
Froome, who won the Tour de France in July, abandoned last Sunday's world championship road race in soaking conditions along with his seven British team mates.
The Tour of Lombardy is the World Tour's (elite) penultimate race of the season.
Froome leads the World Tour standings with an 80-point advantage over Spain's Joaquim Rodriguez of the Katusha team.