The Southampton full-back and Blackpool forward have withdrawn from the squad - which is being coached by senior team manager Roy Hodgson - with knee and groin injuries
Shaw limped out of Southampton's pre-season friendly victory over Real Sociedad with a suspected knee ligament injury.
Ince, meanwhile, who is currently serving a suspension and is unavailable to feature for Blackpool, is understood to be suffering from a minor groin injury.
Everton defender Luke Garbutt has been called up to replace Shaw.
England manager Roy Hodgson and his coaching staff - assistant Ray Lewington and Gary Neville - have taken charge of the Under-21 set-up while the Football Association seeks to appoint a replacement for Stuart Pearce.
The squad also features Manchester United quartet Jesse Lingard, Michael Keane, Tom Thorpe and Sam Johnstone, as well as Liverpool winger Raheem Sterling, Anfield defender Andre Wisdom and Swansea midfielder Jonjo Shelvey.