The Coventry City midfielder has withdrawn from the game in Tirana after contracting a virus.
He has been replaced by Michael O'Connor and is now a doubt for City's game at Peterborough United on Saturday.
Former Coventry City keeper Jonny Tuffey picked up his fifth cap when he came on as a 71st minute substitute in a 1-0 defeat. Skelka scored the only goal with a 26th minute free kick.
A number of City supporters were at Wembley to see England beat Egypt 3-1 with a brace from Peter Crouch.