Jones was ruled out of the remainder of the Autumn Nations Series, as he requires surgery due to the damage done in a crushing 54-16 defeat to New Zealand last weekend.
Wales coach Wayne Pivac does not expect the most capped player of all time to play any part when the defending champion bids to retain its Six Nations title next year.
"I don't think he'll be available for the Six Nations," Pivac said. "You learn a lot about the worth of people when they're not there. I think a lot of people take Alun Wyn for granted – he's always been there and got seniority.
"That leadership is really important. The essence is on others to step up and take that role on."
Jones, who astonishingly recovered from a shoulder injury to captain the British and Irish Lions in South Africa, is in the twilight of his career at the age of 35.
Pivac believes the inspirational towering lock, who won a world record 149th Wales cap in the loss to the All Blacks, can play in the 2023 Rugby World Cup in France.
"The intention is always to see if Al can get to the World Cup. I think it's a realistic goal personally," the New Zealander said.
"You've just got to see him in training and when he's playing, the efforts he puts in. I don't see anything going anywhere near backwards in terms of his performances.
"A bit of time off, we spoke about this before Al left camp. It's not ideal for him. We're all looking forward to him playing 150 Test matches for Wales, but that is still a goal and I'm sure he'll get there."
Pivac has made six changes to the starting XV for the showdown with South Africa at the Principality Stadium on Sunday (AEDT), with Ellis Jenkins replacing Ross Moriarty (shoulder) in what will be his first Test for three years after recovering from a knee injury.
Dan Biggar returns at fly-half, while wing Louis Rees-Zammit, centre Nick Tompkins and prop Rhys Carre also start and Jonathan Davies takes over as captain.
Wales team: Johnny McNicholl, Louis Rees-Zammit, Jonathan Davies (captain), Nick Tompkins, Josh Adams, Dan Biggar, Tomos Williams; Rhys Carre, Ryan Elias, Tomas Francis, Will Rowlands, Adam Beard, Ellis Jenkins, Taine Basham, Aaron Wainwright.
Replacements: Bradley Roberts, Wyn Jones, WillGriff John, Ben Carter, Seb Davies, Gareth Davies, Gareth Anscombe, Liam Williams.