Emergency services resumed their search on Friday morning after being hindered by poor weather and difficult terrain.
The crashed Cirrus SR20 took off from Bankstown Airport in Sydney's southwest on Thursday and appeared to be on its way back when an emergency location transmitter was activated about 4.30pm.
The wreckage was spotted from the air in the Budawang National Park, about 25km north of Batemans Bay on the NSW South Coast, about 5.30pm.
On Friday night, NSW Police said the pilot had been found.
"About 2pm today, a body - believed to be a 60-year-old man - was located at the site, and a recovery operation has concluded with assistance from PolAir and Police Rescue," police said in a statement.
Earlier, NSW Police Inspector David Cockram told reporters that rescuers had scoured "pretty full-on terrain".
"Last night we had fog that prevented the aircraft being able to deploy people down into that exact location," he said.
Multiple agencies including NSW Ambulance, SES and Rural Fire Service members were involved in the search.
Budawang National Park is declared a wilderness area, with hiking, river camping, swimming and scenic views for advanced, well-equipped travellers.
The pilot was believed to have been the only person on board the plane, which comes in four- or five-seat configurations.
The Cirrus SR20, first manufactured in 1999, is notable for being equipped with a "whole-plane" parachute system.
The plane had been rented, Insp Cockram said.
An investigation into the cause of the crash will be conducted by the Australian Transport Bureau.
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