The withdrawal of the Manchester United centre-back further worsened manager Gareth Southgate's defensive woes, with Phil Jones also unavailable and Gary Cahill suspended.
Gibson has impressed in his first season in the Premier League and was a regular for England's Under-21 side under Southgate's tutelage.
Southgate had not been planning to call up any reinforcements for Sunday despite the absence of Cahill and Jones, but Smalling's unspecified setback has forced his hand ahead of Sunday's World Cup qualifier.
"We'll just assess over the next 24 hours if we have picked up any other knocks," the England boss said following Wednesday's loss to Germany.
"I am not aware of anything significant at the moment so if that is the case we wouldn't."
Smalling has returned to Manchester to undergo treatment.
Unbelievable honour to be called up to the England squad. Very proud moment for me and my family ❤️ thanks everyone 👌🏻 #comeonEngland— Ben Gibson (@bengibson1993) March 24, 2017
England trained in Hertfordshire on Friday and Gibson will take part in Saturday's session at Tottenham's training base, where Southgate will speak to the media.