Raheem Sterling has been replaced in the England squad by Crystal Palace winger Andros Townsend.
Sterling was withdrawn after City confirmed news of the unspecified injury believed to be a calf strain.
The injury is not believed to be serious and Sterling should be fit to return after the international break.
The Manchester City winger, who had been in a rich vein of form recently, could not prevent City’s first defeat of the season in the top of the table clash at Spurs on Sunday.
England caretaker manager Gareth Southgate had earlier named Manchester United players Marcus Rashford and Jesse Lingard in his squad alongside other senior Manchester based players such as Chris Smalling and John Stones.
Rashford was promoted back to the senior team after just one game in the Under-21 setup in which he scored a hat trick against Norway.
The uncapped Jesse Lingard was also named in the squad.
And Southgate confirmed that Wayne Rooney would remain captain of the national team.
There was one surprise, with Stoke’s 32-year-old right full back Glen Johnson earning his first call-up in two years.
England face Malta at home on October 8 and Slovenia away on October 11.
UPDATED ENGLAND SQUAD
Goalkeepers: Fraser Forster (Southampton), Joe Hart (Torino, on loan from Manchester City), Tom Heaton (Burnley)
Defenders: Ryan Bertrand (Southampton), Gary Cahill (Chelsea), Phil Jagielka (Everton), Glen Johnson (Stoke), Danny Rose (Tottenham), Chris Smalling (Manchester United), John Stones (Manchester City), Kyle Walker (Tottenham)
Midfielders: Eric Dier (Tottenham), Jordan Henderson (Liverpool), Alex Oxlade-Chamberlain (Arsenal), Michail Antonio (West Ham), Jesse Lingard (Manchester United), Theo Walcott (Arsenal), Dele Alli (Tottenham), Andros Townsend (Crystal Palace)
Strikers: Wayne Rooney (Manchester United), Marcus Rashford (Manchester United), Daniel Sturridge (Liverpool), Jamie Vardy (Leicester)