Welbeck sustained the injury in the second half of the victory at Wembley and was replaced in the 77th minute.
The FA confirmed on Saturday that Welbeck had been sent back to Arsenal and therefore will not feature in England's friendly against Italy in Turin on Tuesday.
The FA also confirmed Raheem Sterling, James Milner and Leighton Baines had been sent back to their clubs.
Liverpool forward Sterling is carrying a toe injury and Manchester City midfielder Milner did not play against Lithuania as he had a knee problem.
Baines has gone back to Everton as Roy Hodgson wants to give Kieran Gibbs his seventh cap in Turin.
GETTY
Danny Welbeck has been ruled out of the England squad
The England manager has called up Southampton's Ryan Bertrand as cover for the Arsenal defender.
“We knew we were going to be losing Raheem Sterling who had an injection last night on an on-going injury and hopefully that will help him as we go forward," said England boss Hodgson.
“We have a problem with James Milner who had to leave, we decided to let Leighton Baines go home and of course we lost Danny Welbeck, who unfortunately picked up a slight knee injury [against Lithuania].
“So those four players won’t be with us going forward but it means a chance for the other guys in the squad to show what they can do.
“We are going to bring Ryan Bertrand in because with Leighton Baines gone we are now left with only one recognised left-back, which is Kieran Gibbs and we wanted two recognised left-backs for both games.”
The updated England squad
Goalkeepers
Jack Butland (Stoke City), Robert Green (Queens Park Rangers), Joe Hart (Manchester City)
Defenders
Ryan Bertrand (Southampton), Gary Cahill (Chelsea), Nathaniel Clyne (Southampton), Kieran Gibbs (Arsenal), Phil Jagielka (Everton), Phil Jones (Manchester United), Chris Smalling (Manchester United), Kyle Walker (Tottenham Hotspur)
Midfielders
Ross Barkley (Everton), Michael Carrick (Manchester United), Fabian Delph (Aston Villa), Jordan Henderson (Liverpool), Ryan Mason (Tottenham Hotspur), Andros Townsend (Tottenham Hotspur), Theo Walcott (Arsenal)
Forwards
Harry Kane (Tottenham Hotspur), Wayne Rooney (Manchester United)
Invalid email
We use your sign-up to provide content in ways you've consented to and to improve our understanding of you. This may include adverts from us and 3rd parties based on our understanding. You can unsubscribe at any time. Read our Privacy Policy
