It is another blow for the 25-year-old, who has yet to make his full international debut having also been forced to pull out of the game with England at Wembley at the end of last season.
Goalkeeper David Forde is to be replaced by West Ham's Stephen Henderson, while Nottingham Forest forward Simon Cox is also sidelined.
A statement from the Football Association of Ireland read: "The Football Association of Ireland today confirmed that David Forde has withdrawn from the Ireland squad to face Wales in Cardiff on Wednesday, August 14 after undergoing surgery following a knee injury sustained with Millwall on Saturday.
"West Ham's Stephen Henderson has been called up as a replacement, and will report for training with the squad in Newport on Sunday.
"Anthony Pilkington has withdrawn from the squad also after picking up a knee injury during pre-season training with Norwich. Along with Simon Cox, who suffered an ankle injury during Nottingham Forest's Capital Once Cup win last night.
"Updates will be issued in due course should replacements be added."
Striker Robbie Keane had been left out of the initial 26-strong squad for the friendly fixture as he is in action with Los Angeles Galaxy
in the United States, while centre-back Richard Dunne continues to work on his match fitness after joining QPR from Aston Villa in the summer.
There was also no place for Wolves striker Kevin Doyle.
Manager Giovanni Trapattoni is looking to continue the good form of 2013, where they were unbeaten until the 2-0 defeat to Spain in New York at the start of June, claiming impressive victories over Georgia and the Faroe Islands and holding England to a 1-1 draw at Wembley.
"We can draw a lot from our performances in May and June. The team showed strong character and enthusiasm against Spain, England and Georgia, and picked up three vital points against the Faroe Islands," the Italian said when naming his provisional squad last month.
"The players have demonstrated that they are building on each game and are working very well together.
"This fixture will allow us one more opportunity to prepare for the important World Cup qualifiers in September against Sweden and Austria. We will use this time to experiment and develop confidence ahead of the games."
Ireland host Sweden on September 6 and then travel to Austria looking to keep up the chase for second spot in Group C, where three sides are locked on 11 points, five behind leaders Germany after six matches.