The incident took place Friday morning in the 5500-block of South Normandy.
The officer heard someone knocking on his door, but when he went to check it out the person walked away. Then a guest who was staying with him left the house and the officer heard someone break in.
"The officer dials 911 to alert police that someone's breaking into his house. As he's on the phone, he is confronted now by this offender with something in his hand, and the officer fires at the offender, striking him multiple times, and the offender is DOA," said Eddie Welch, Chicago Police Department.
The man who died had allegedly kicked in the home's basement door.
The officer had been at home recovering from an unrelated injury. He was not hurt as a result of the break-in.
The Independent Police Review Authority is investigating.