Club officials told reporters at Shielfield Park that McGinn was being rested for the match along with Marvin Bartley, Darren McGregor and striker Florian Kamberi.
The Easter Road outfit this week rejected a £1.5 million bid for the player from the Glasgow club but are bracing themselves for an improved offer.
McGinn, 22, is rated at £4m by Hibs but is entering the final year of his contract, having joined from St Mirren in 2015.
Hibs team to face Berwick: Bogdan, Gray, Whittaker, Hanlon, Ambrose, Stevenson, Martin, Slivka, Swanson, Shaw, Murray. Subs: Laidlaw, Stirling, Boyle, Allan, Mackie, Gullan.