The resident has not been charged in the shooting, though the case is still under investigation.
The incident happened at a house on the 34000 block of Capistrano By the Sea in Dana Point.
At least two bullets shattered a window at the house. Authorities say at least one bullet hit the male intruder who allegedly confronted the victim around 11 p.m. Monday.
"The homeowner heard some noises inside his home, checked around initially, did not see anything. Went back into his bedroom, heard some more noises," said Jim Amormino, spokesman for the Orange County Sheriff's Department.
Investigators say the resident then armed himself with a handgun and opened his bedroom door, where the suspected burglar confronted him.
"I'm not sure how many shots were fired, but more than one shot was fired by the homeowner," said Amormino.
Authorities say the suspect managed to climb out an open window that he originally came through, then died in the back yard.
Authorities say the suspect was not armed. It was not clear why he targeted that residence.
"He shot the intruder and I do feel that if you're in your home you have a right to protect yourself because you don't know what they're going to do to you," said Dana Point resident Marlene Lopez.
Investigators are trying to determine exactly what led up to the shooting.
"The law reads that at some point you have to show that you're in fear of your life and that you were in danger," said Amormino. "That part is still under investigation."
The suspect's and the homeowner's identities were not released.