Fiji is yet to appear in the new tournament because of a coronavirus outbreak in its camp.
Its opener against France was called off, with Les Bleus handed a 28-0 bonus-point win, before last week's clash with Italy likewise fell by the wayside amid 29 COVID-19 cases.
Tournament organisers have now confirmed more than a week in advance that Scotland will not be able to face Fiji either, describing the decision as "unavoidable".
Fiji will finish bottom of Group B but has one match remaining on 6 December (AEDT) against the fourth-placed team in the other pool.
This will be "subject to checks on fitness levels once the players come out of isolation and following all appropriate protocols", an Autumn Nations Cup statement read.
It added: "The tournament organisers remain in constant contact with the Fijian squad regarding their wellbeing and recovery, which continues to be the number one priority."