He will be replaced by the experienced Liam Williams (31), who was not in the original matchday 23 named by coach Warren Gatland on Tuesday as he too works his way back to fitness having played only 180 minutes this season due to injury.
It is another setback for Halfpenny and his Rugby World Cup chances after he was also named to start against New Zealand and Australia in the autumn internationals late last year, but had to withdraw on each occasion.
It is now 19 months since his last start following a knee injury sustained against Canada in July 2021.
"Unfortunately, Leigh had a back spasm this morning and Liam will be playing," Wales forward coach Jonathan Humphreys told reporters on Thursday.
"I think it's more disappointing for him as a person. He's had a couple of these recently. He's an unbelievable professional and an unbelievable person.
"He's got to pick himself up again. You feel for him that he's got to pull out at this late stage again."
Wales team: 15-Liam Williams, 14-Josh Adams, 13-George North, 12-Joe Hawkins, 11-Rio Dyer, 10-Dan Biggar, 9-Tomos Williams, 1-Gareth Thomas, 2-Ken Owens (capt), 3-Tomas Francis, 4-Adam Beard, 5-Alun Wyn Jones, 6-Jac Morgan, 7-Justin Tipuric, 8-Taulupe Faletau.
Replacements: 16-Scott Baldwin, 17.-Rhys Carre, 18-Dillon Lewis, 19-Dafydd Jenkins, 20-Tommy Reffell, 21-Rhys Webb, 22-Owen Williams, 23-Alex Cuthbert.
