Essex County prosecutors say the shooting occurred around 2:35 a.m. Friday at the officer's home.
The officer, whose name was not released, discovered the burglary in progress and approached the man, identified as 19-year-old Robert Robinson of Newark. Robinson allegedly waved an undisclosed object at the officer, who fired his service weapon.
Robinson was treated at a hospital for his wounds and released later Friday. He's charged with aggravated assault, burglary and weapons offenses.
The officer was not injured.
Authorities did not provide further details on the shooting, which remains under investigation.