Spartak Moscow winger McGeady was named in Trapattoni’s provisional 29-man squad but was forced to pull out due to a knee injury.
The Football Association of Ireland also confirmed Hull defender McShane, who has an ankle injury, and Norwich winger Pilkington, sidelined with a hamstring strain, will miss the trip to face Sweden in Stockholm next Friday and the clash against Austria in Dublin four days later.
Sweden also face injury problems ahead of the match with Zlatan Ibrahimovic the only recognised striker who is fully fit. IFK Göteborg striker Tobias Hysén is in the running for a start although he is in the midst of pre-season training.
Ola Toivonen is the only other alternative after he survived a come back from five months injury for PSV Eindhoven in the Dutch league on Saturday. The 27-year-old came off before the end in order to protect his chances of playing in Friday’s clash.
Johan Elmander, Alexander Gerndt, Marcus Berg, Markus Rosenberg and Mathias Ranegie are all unavailable through injury or loss of form.
The match is a must-win for Sweden if they are to maintain their hopes of featuring in the finals in Brazil next year.
Ireland’s chances of qualifying for Brazil are meanwhile slim after a shaky start to their campaign.