Halfpenny was due to win his 98th cap and make a first Wales start for 19 months, but assistant coach Jonathan Humphreys said he had suffered a back spasm and would miss the game.
Experienced Cardiff back Liam Williams will replace Halfpenny in the number 15 shirt.
Williams missed Wales’ entire Autumn Nations Series campaign this season because of injury, and has not started for his country since last summer’s South Africa tour.
Humphreys said: “Unfortunately, Leigh had a back spasm this morning and Liam will be playing.
“I think it’s more disappointing for him as a person. He is an unbelievable professional and an unbelievable person.
“He has got to pick himself up again. You feel for him that he’s got to pull out at this late stage.
“Liam is good to go.”