The 23-year-old Welshman has already been ruled out for the remainder of the current season but the operation has been declared a success.
Glen Driscoll, Liverpool's head of performance, told the club's official website on Thursday: "Joe Allen had surgery this morning, which went very well.
"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 fighting fit for the start of pre-season."
Allen has been troubled by the injury to his left shoulder since November last year, and he aggravated the problem in Saturday's 3-1 defeat at Southampton.