The 23-year-old had already been ruled out for the rest of the season with the injury and the operation will allow the No.24 to be 'fighting fit' for pre-season ahead of the 2013-14 campaign.
"Joe Allen had surgery this morning, which went very well," head of performance Glen Driscoll told Liverpoolfc.com on Thursday.
"It's going to be a relief for Joe that this has now happened for him. It has been quite a long-standing issue. He was repetitively subluxing, so his shoulder was coming out very easily and very often.
"It was a procedure that was very important. He should be 12 weeks from now, so he'll be fighting fit for the start of pre-season."
Driscoll explained the extent to which the injury was affecting Allen, who has played matches without knowing where and when the problem might recur.
He added: "I think he has done amazingly well. Anyone who has ever had repetitive subluxations of shoulders will know there is a lot of apprehension involved.
"I find it difficult to see how that wouldn't have affected Joe. It was getting to the point where he would do a high-five to celebrate a goal and would actually feel a sublux.
"When you know this is happening, it's not just the pain that occurs - it's the apprehension.
"He has done very well to get through this and it's great for him that we can draw a line under this, get him fit and see how he goes next season."