The 27-year-old suspect was shot in the head and is in a critical condition.
According to police he had stolen the key to the house from the owner's office, where he had been briefly employed in 2014.
He entered the home early on Friday morning, around 3.30am, but the owner heard him and woke up.
He then shot at the intruder with a handgun, down an unlit staircase. The 37-year-old man had a license for the gun.
The case has been handed over to the St. Pölten prosecutor and an investigation is ongoing.