Points leader Max Cook was back on top as the rain stopped at Knockhill, clocking a 53.069sec lap to beat Sam Laffins to the top spot.
Asher Durham finished the session third, just ahead of Holdsworth as Seth Crump just beat Franco Bourne to fifth.
Pirelli National Junior Superstock Championship with MotoNovo Finance, Knockhill, FP2
1. Max Cook (Uggly & Co by Binch Pro)
2. Sam Laffins (Cheshire Mouldings Kawasaki by JR Performance) +0.138s
3. Asher Durham (Completely Motorbikes/Affinity) +0.387s
4. Joe Holdsworth (Holeshot Kawasaki Yeovil) +0.572s
5. Seth Crump (Seeeeeth) 0.767s