The woman told officers she was fine, and showed identification, but winked at the officer to alert him that something was wrong, police spokesman Lt. John Stanford said.
The officer again asked the man for his ID, Stanford said. At that point, the man pulled out a handgun and held it to the officer's head, Stanford said.
The officer was able to knock the gun away with his hand - the weapon discharged as he did so - and pull his own weapon, shooting and killing the man, Stanford said. Stanford could not say how many shots were fired.
The man was pronounced at the scene by medics at 1:02 a.m.
"This officer, we're lucky we're not planning a funeral," Stanford said. "This officer was sharp enough to recognize this woman was in distress. It was an outstanding job."
Police said a weapon was recovered at the scene.
The man killed by the officer had targeted the home with an accomplice, waited for the couple who lived there to arrive home and forced them into the house at gunpoint - tripping the burglar alarm as they did so, Stanford said.
The accomplice fled the scene and police were still looking for him, Stanford said. He described the suspect as a Hispanic male, and said police were combing the house for fingerprints and searching the area.
Police also towed away a silver Mazda car.
Stanford said the man who was killed was 42 years old and had lived on the 1400 block of St. Vincent Street in Castor Gardens. He would not release the man's name, because his family had not yet been notified, but said he had 12 prior arrests in connection with robbery, firearms violations, receiving stolen property and narcotics offenses.