It happened at 12 a.m. Tuesday in the 800 block of East Sanger Avenue.
Police say two boys walked into Kenny's Beer Place to buy beer.
The 27-year-old owner asked to see identification, and the boys refused.
That's when, police say, the teens started to trash the store, throwing boxes and other objects around.
The vandalism continued behind the store.
Police say the store owner then grabbed a semi-automatic weapon and fired one shot, hitting the 16-year-old.
The bullet when through both of his hands. Police say the teen likely had his hands up for cover.
Both boys then fled on foot. The gunshot victim later turned up at Jeanes Hospital, where he received treatment.
The other boy remains at large.
Investigators say they have surveillance video of the entire incident and are examining the images for clues.
The store owner was taken in for questioning, and was still be questioned as of noon. It is not clear if he will face any charges.