Prop WP Nel (arm fracture) and lock Tim Swinson (hand) will miss the remainder of 2017, which also includes a test against Australia on November 25, after picking up injuries in the 44-38 victory over Samoa on Saturday.
Flanker Rob Harley, who injured his knee in training last week, will also not feature again this year.
Newcastle Falcons prop Jon Welsh has been added to the squad as cover and could play his first test in more than two years having last appeared in the 2015 Rugby World Cup quarterfinal loss to Australia at Twickenham.
Wing Tommy Seymour is also in line to feature against the All Blacks after an MRI scan on his toe revealed an injury sustained against Samoa was not as bad as first feared and he should resume training this week.
Scotland went into the internationals without 10 regulars, including props Alasdair Dickinson, Allan Dell and Gordon Reid, and hookers Fraser Brown and Ross Ford.
The side has also been without influential halfback Greig Laidlaw and lock Richie Gray.
Scotland have never beaten New Zealand, with their 30 previous meetings resulting in two draws and 28 defeats.
Photo by: GETTY IMAGES. Caption: WP Nel joins Scotland's long casualty list ahead of their test against the All Blacks.