The full-back is thought to have strained his groin.
Hogg has been in outstanding form during the autumn series, helping Scotland beat Samoa before losing narrowly to world champions New Zealand.
Sean Maitland has switch from wing to full-back to replace the Hawick man, with Byron McGuigan of Sale likely to step off the bench to take Maitland’s wing berth.
It will be South African-born McGuigan’s first start for Scotland.
The versatile Ruaridh Jackson is added to the replacements.