The experienced defender has been an integral part of the first team so far this campaign, but faces a prolonged spell on the sidelines due to the thigh issue
The centre-back sustained a muscular problem in training earlier this week, and underwent a series of tests on Wednesday to determine the extent of the knock.
The Rossoneri have now announced that Bonera has suffered a thigh injury, and will be out of action for a while as a result.
"AC Milan have announced that Daniele Bonera has suffered a thigh tear in his left leg and the defender will undergo further tests in two weeks to gauge his progress," an official statement confirmed.
Bonera, 31, has made 13 official appearances for the Rossoneri this term, receiving seven yellow cards in the process.