The officer-involved shooting happened outside a home in the 7900 block of Merrington Place.
Police say the nude burglar jumped at the officer who was responding to a 9-1-1 call placed by the woman who fled her home when she saw the burglar.
"During this attack the officer dropped his gun, both individuals were trying to get the gun... somewhere in between officer attempted to taser the suspect with negative results, the officer was able to grab the weapon and fire one round," said Capt. Al Guaderrama of San Diego Police Homicide.
The suspect was shot in the chest and taken to a hospital where he is listed in critical condition according to Capt. Guaderrama.
Investigators are trying to figure out what the suspect was doing and why he was trying to break into the home.