The Stoke City goalkeeper had been widely tipped to start the game against the world champions at Wembley but now adds to a lengthy injury list for boss Gareth Southgate.
Tottenham trio Harry Kane, Dele Alli and Harry Winks, Manchester City duo Raheem Sterling and Fabian Delph and Liverpool captain Jordan Henderson have all withdrawn from the squad through injury since being selected.
Chelsea's Danny Drinkwater declined a call-up on fitness grounds.
Southgate has announced Eric Dier will captain the Three Lions in the absence of his Spurs colleagues.
bit of luck wouldn’t go a miss, but can’t keep me down for long! be back soon— Jack Butland (@JackButland_One) November 9, 2017
Butland, who has returned to Stoke to be assessed by his club's medical staff, sustained a broken ankle when England faced Germany in March 2016.
That injury and multiple further complications kept the 24-year-old out of action for more than a year but he has been an ever present for Mark Hughes' side in the Premier League this season.