The area around the Rafidia hospital was sealed off by security forces as they defused the device inside the vehicle which had been parked just inside the compound.
Witnesses said the vehicle had been left at the hospital, the largest in the northern West Bank, for about three days.
Many of the patients were carried out of the hospital by wheelchair and stretcher, but they were allowed to return after less than 30 minutes when the explosive device in the car was made safe.
Nablus has been the scene of some of the fiercest fighting of the five-year Palestinian uprising against Israel.
Its residents last week elected Hamas, the Islamist group behind most anti-Israeli attacks since 2000, to govern their municipality.