The 29-year-old has flown home from the Wallaby training camp and will also miss the following week's fixture with Argentina in Rosario.
Moore sat out both home games against the Springboks and Pumas earlier this month after an initial hamstring strain but it was hoped he would be fit to challenge Tatafu Polota-Nau for a starting spot at Loftus Versfeld.
The veteran Brumbies star is just one cap away from overtaking Jeremy Paul as Australia's most-capped hooker and he was expected to reach that milestone from the bench this weekend.
But he will now have to wait until the Bledisloe Cup tie with New Zealand in Brisbane on October 20 or the autumn tour of Europe to rewrite the history books.
Moore's absence means Polota-Nau is almost certain to start on Saturday, with Saia Faingaa of the Reds set to feature among the replacements even though the uncapped James Hanson has been flown to South Africa as cover.
The news is the latest in a long line of injury setbacks for the Lions' next opponents who already have the likes of James Horwill, David Pocock and Will Genia on the sidelines.
Drew Mitchell, Cooper Vuna, Joe Tomane, Wycliff Palu and Ben McCalman are also injured, as are star names James O'Connor and Quade Cooper.
Wallaby head coach Robbie Deans is delaying naming his team for this weekend until he and his coaching staff are convinced second rower Sitaleki Timani has overcome a troublesome stomach bug.