De Groot has failed to recover from a neck injury which ruled him out of the test against Argentina last Saturday.
He will be replaced in the squad by Otago’s George Bower, who was due to play for his province against Bay of Plenty in the NPC tomorrow.
Bower, 32, played the first of his 21 tests in 2021 but was not part of the original squad to tour South Africa named by new coach Scott Robertson.
New Zealand take on the world champions at Ellis Park in Johannesburg on 31 August and a week later in Cape Town.
South Africa have a maximum 10 points from their opening two wins over Australia, five more than New Zealand.
- Additional reporting Reuters