The Wales fly-half suffered a double twist playing for his French club side Clermont Auvergne.
An MRI scan indicated Jones had not broken anything but medical advice suggests he will need four weeks to recover and Wales take on the All Blacks on November 5.
A club spokesman said: "We hope he will be fit for the internationals but he has a twisted left ankle and he probably won't be able to play for four weeks.
"He had an examination and nothing is broken but we saw a double twist."
Wales take on New Zealand in a Test to mark the centenary of the first international between the two sides.
The Six Nations champions then face Fiji and South Africa before ending their autumn programme against Australia.
But the injuries are mounting up for head coach Mike Ruddock, who is already without British & Irish Lions duo Gavin Henson and Gethin Jenkins for the whole series.
Flanker Dafydd Jones is also out while Shane Williams and Ryan Jones, who both featured for the Lions in New Zealand this summer, are rated 'highly doubtful' by the Welsh Rugby Union.
Fellow Lion Tom Shanklin has not played yet this season as the centre rests an injured knee.
If Jones is ruled out of the All Blacks game then Ruddock may well turn back to Cardiff's in-form fly-half Nicky Robinson.
The 23-year-old filled the number 10 jersey for Wales' summer victories over the USA and Canada when Jones was away with the Lions.
He scored 22 points in Cardiff's Powergen Cup victory over Saracens.
Ruddock was watching from the stands and after the game Blues coach Dai Young said: "The talent he's got and his distribution skills put him out in front of most 10s.
"The biggest thing he has had to work on is his game awareness and I think he has done that extremely well.
"You don't want to sit on him and stifle that attacking flair.
Obviously he has put years on me as a coach on occasions. But I think that is what quality players tend to do."