The suspect, Alex Debono, 20, of 464 Route 25A in Miller Place was stabbed as he tried to escape through the backyard of the home at Cedar Oaks Avenue at about 2:15 p.m., police said.
The homeowner discovered Debono climbing out of a rear window and confronted him with a knife after noticing the suspect had a knife, police said.
Debono escaped after he climbed over a fence and fled to a nearby Kmart, police said, adding that he was arrested by Sixth Precinct Patrol Officer Daniel Furey at the store at 2280 North Ocean Ave. in Farmingville.
Some of the items police said were taken from the home include a watch and an Xbox, which were recovered in the store's bathroom.
Debono was treated for his wound at Stony Brook University Hospital. He is charged with first-degree burglary and fourth-degree criminal possession of a weapon.
He is scheduled to be arraigned Tuesday in First District Court in Central Islip.