Smalling joins Phil Jones in having returned to Old Trafford after his team-mate picked up an injury that ruled him out of Wednesday's clash with Germany.
Fellow defender Gary Cahill will also miss the match through suspension, meaning Middlesbrough's Ben Gibson earns his first call-up to the national side.
Gibson has previously made 10 appearances for the England Under-21s, most of which came under current Three Lions boss Gareth Southgate.
He joins Michael Keane and John Stones as the only centre-backs in the squad, meaning a debut is likely at Wembley on Sunday.
Southgate operated with a three-man backline against Germany, though Eric Dier could be drafted into the defence if the Three Lions boss wants to keep Gibson on the bench.
England had been on a five-game unbeaten run since their humiliating Euro 2016 defeat to Iceland before Germany brought that sequence to an end with a 1-0 win in Dortmund.