Shaw limped off in the first half of Southampton's pre-season friendly against Real Sociedad on Saturday with suspected knee ligament damage.
It is the fourth time that the uncapped left-back has had to withdraw from the U21 squad due to injury.
No reason has been given for Ince's withdrawal, although the Blackpool forward has been suffering with a groin injury of late.
Everton's Luke Garbutt has been drafted in to the squad as a replacement.
Roy Hodgson led a training session at St George's Park on Sunday morning, ahead of the fixture at Sheffield United's Bramall Lane.
The England boss has agreed to take charge of the Young Lions as the Football Association continues to search for a long-term replacement for Stuart Pearce, whose contract was not renewed following the team's disappointing European Championship campaign.