Jones chipped a bone in his right elbow while making a tackle on Scottish centre Sean Lamont before the end of Wales' 31-24 RBS 6 Nations win at the Millennium Stadium.
As well as chipping the bone, Jones also suffered ligament damage and the decision was made for him to undergo surgery which will sideline him for between six and 12 weeks.
"Alun Wyn experienced some swelling to the joint the day after the game and was sent for a scan, after receiving those results and after further consultation with surgeons today, it has been concluded that the chipped bone needs to be removed and the ligament to be repaired in order to ensure a stable joint," said Wales physio Mark Davies.
"The necessary period of recovery will be six to 12 weeks ruling him out of the rest of the current 6 Nations and allowing him to target an end of season return for the Ospreys."
The Ospreys are currently lying in second place in the Magners League regular league campaign and are targeting a top four finish to guarantee a place in the Play-Offs.
Jones' injury is the latest blow for the Welsh squad during the 2010 RBS 6 Nations championship. On Monday the Cardiff Blues back row forward Andy Powell was dropped from the squad after being arrested on a drink drive charge hours after the victory over Scotland.