The Football Association of Ireland confirmed the news on Saturday afternoon.
Spartak Moscow winger McGeady has been suffering from an ongoing ankle injury for much of the season.
Pilkington pulled his hamstring after 24 minutes of Norwich's goalless draw with Queens Park Rangers at Loftus Road.
Norwich boss Chris Hughton said: "Pilkington has a hamstring injury. We will assess how bad it is, but at the moment certainly we will be pulling him out of the Irish squad."
The FAI said both players will remain at their clubs for treatment and an update will be issued later today should Giovanni Trapattoni decide to call in any replacements.