In the first of two hour-long, all-in sessions it was Winkelhock that led the way in the #777 Melbourne Performance Centre Audi.
The German gapped the field by just over half a second with a rapid 2m03.133s, the fastest time of the weekend so far.
Ben Barker was second fastest in the #4 Grove Racing Porsche ahead of reigning Bathurst 12 Hour winner Jules Gounon (#75 SunEnergy1 Racing Mercedes) while David Reynolds (#24 MPC Audi) also dipped into the threes.
The first session saw trouble for the #17 Team BRM Audi which crashed heavily with Mark Rosser at the wheel.
The car didn't take part in the second session and is in doubt for qualifying later today.
In the second session it was van der Linde that set the pace with a 2m03.257s in the #74 MPC Audi.
That time came relatively early in the session with nobody able to run it down.
The closest anybody got was Chaz Mostert in the #65 MPC Audi who ended up just over two-tenths off the pace.
That left the reigning Bathurst 1000 winner just clear of Gounon and Cam Waters in the #24 MPC Audi.
Ricardo Feller led the way early in the #777 MPC Audi but slipped back to fifth ahead of Shane van Gisbergen in the #888 Triple Eight Mercedes and David Wall in the #6 Wall Racing Lamborghini.
The Grove Porsche was eighth fastest in the second session but ended up in the wall at Reid Park with Stephen Grove behind the wheel.
Meanwhile the Craft-Bamboo Mercedes is yet to turn a lap today and is in serious doubt for qualifying thanks to an engine problem.
The car is currently undergoing an engine change at a workshop in the Bathurst township and is expected to be ready for tomorrow's race.
The #47 Audi, which crashed heavily in practice yesterday, is also expected to return for the race after MPC freighted a spare chassis to from Melbourne to Mount Panorama overnight.
The spare car is currently being upgraded to EVO II spec.
Qualifying for the Bathurst 12 Hour kicks off at 1:20pm AEST.
Tune in to watch it live and free on Motorsport.tv (not available to viewers in Australia and New Zealand).
