Jones, a pivotal performer during Wales' successful World Cup campaign in New Zealand, will undergo surgery this weekend after suffering a foot injury during training with the Ospreys.
He has not travelled to Italy with the Ospreys squad for Saturday's Heineken Cup fixture against Treviso.
Wales and hooker Huw Bennett, meanwhile, is also out of the Treviso game. He suffered a neck spasm during last Saturday's Pool Five victory over Biarritz.
"Alun-Wyn suffered a foot injury in training this week," Ospreys head physiotherapist Chris Towers said.
"As a result, he is going to require surgery to repair soft tissue damage, which will be carried out over the weekend.
"Once he starts his post-op rehab work we will be in a better position to predict recovery timelines.
"Huw, unfortunately, didn't recover in time from a neck spasm that developed after last weekend's game to be considered to play against Treviso."
Gatland is due to name a 26-man squad for the December 3 Australia Test on Sunday.
It is a quickfire rematch between the countries after Australia narrowly defeated Wales in the World Cup bronze medal match at Eden Park, Auckland just four weeks ago.
Jones' Wales' second-row partner Luke Charteris is currently recovering from a wrist injury, while flanker Dan Lydiate suffered ankle trouble in Newport Gwent Dragons' Amlin Challenge Cup success against Cavalieri Prato six days ago and was forced off.
The opening round of European action also saw Cardiff Blues centre Jamie Roberts take a knock, although he is expected to regain full fitness in time for the Wallabies' Cardiff visit.
In addition to the injury situation, Gatland looks set to be without France-based trio Mike Phillips, James Hook and Lee Byrne.
Phillips (Bayonne), Hook (Perpignan) and Byrne (Clermont Auvergne) all linked up with their new clubs following the World Cup, but as the Australia game is outside the International Rugby Board's official Test match window, non-Welsh clubs are under no obligation to release players unless individual contracts allow it.
Bayonne, Perpignan and Clermont are all in French Top 14 league action on December 3, while Aviva Premiership commitments the same weekend could sideline Exeter prop Craig Mitchell, plus Sale Sharks pair Andy Powell and Dwayne Peel.