The Ospreys skipper will miss his side's Heineken Cup clash with Benetton Treviso on Saturday and faces an anxious wait before finding out how long he will be kept on the sidelines.
Wales face Australia in a rematch of the third-place play-off encounter at the recent World Cup on December 3 but it would now be a major turnaround if Jones was available for selection.
"Alun-Wyn suffered a foot injury in training this week," said Ospreys head physiotherapist Chris Towers.
"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."
The news is a bitter blow for Wales coach Warren Gatland especially as fellow first-choice lock Luke Charteris faces a race against time to recover from a wrist injury.
Charteris' Newport Gwent Dragons team-mate Dan Lydiate is another injury doubt as he nurses an ankle knock, while French-based stars Mike Phillips, James Hook and Lee Byrne are unlikely to be given permission to play in the fixture as it sits outside the IRB window.