And, after a thorough medical review, it was decided the 26-year-old would risk lasting damage if he was not withdrawn from the World Cup.
Jones said: "Having taken advice from the specialist in a review appointment yesterday (Wednesday), following a planned exploratory operation I had 11 days ago, it has been decided it is in my best interests to withdraw from World Cup selection.
"Although the shoulder is stable I received some new damage to the joint throughout this season which needs time to settle.
"I need to take a long-term view and make sure it's right before I play and that means missing out on the World Cup.
"It's obviously bitterly disappointing, but at the age of 26 it would be completely the wrong decision to try to rush myself back to fitness with a high risk that something could go wrong.
"I'm missing the World Cup, which is extremely difficult to take, but it means I will be able to get back to full fitness and turn out and captain the Ospreys next season and ensure I'm still around when its time for the next one.
"We've got a great squad and I can't express how gutted I am to miss out, but I know the boys will do us proud out there, and there are hopefully a good few more years left in me yet."
Jones burst on to the Test scene in Wales' 2005 Grand Slam RBS 6 Nations campaign and shone for the Lions in New Zealand after receiving a late call-up.
He missed the whole of the 2005-06 season after undergoing a shoulder reconstruction and it was no coincidence that Wales struggled in his absence.
Jones returned to action last season and established himself once again as a key figure in the Wales side.
Wales also have injury concerns over Gavin Henson, who has spent the last three weeks trying to overcome an Achilles injury.