Kong-rey slammed into Taiwan's mountainous and sparsely populated east coast on Thursday afternoon, the largest storm by size to hit the island in nearly 30 years, then worked its way across central Taiwan before entering the Taiwan Strait and moving north.
The fire department put the death toll at two - one whose truck was hit by a falling tree in central Taiwan, and another in Taipei who was hit by an electricity pole. It also reported 515 injuries.
Workers in Taipei gradually removed fallen trees which snarled traffic, delaying the arrival of some ministers for a parliament session.
In the Taroko park in Hualien County, rescuers flew to safety in a helicopter two Czech hikers who had been trapped by the typhoon.
Flight disruptions continued on Friday, with 57 international flights canceled along with 135 domestic ones, though the north-south high speed rail link resumed normal operations.
Even after losing power as it traversed Taiwan, Kong-rey remained a severe tropical storm as it entered the Taiwan Strait, bringing strong winds and heavy rainfall to the coastal Chinese province of Fujian.
Kong-rey will likely not make landfall in mainland China but is expected to quickly swing back into the open sea later on Friday towards Japan.