The 27-year-old suffered an injury in the warm-up for Saturday’s 2-1 win against Switzerland, which meant he had to withdraw from the starting XI.
England boss Gareth Southgate is expected to make wholesale changes for Tuesday’s game at Wembley.
Saturday’s team mixed established and inexperienced players, with Tuesday’s expected to follow a similar template.
“We’ll make changes. We think that’s the right thing to do,” said Southgate.
“We want to keep all of the squad involved. I think that has been a strength for us. Players who come in perform well at the level and the team march on.
“They need to feel that we’ve got the confidence in them to go into any game and we’re also at a stage of the season where their load is heavy and we’ve got to make sure we try and navigate that in the best way possible.”
‘It is about the weight of the England shirt and how they cope’
All 24 players took part in training on Monday, including Arsenal’s Emile Smith Rowe, who missed Saturday’s game through injury, and Stones, who was replaced in the starting XI by Ben White after experiencing “some tightness”.
After Monday’s session he returned to his club as a precaution but Southgate confirmed that Harry Maguire will start at Wembley on Tuesday.
Stones is the seventh player to withdraw from Southgate’s squad, with the others including Arsenal pair Aaron Ramsdale and Bukayo Saka, as well as Liverpool right-back Trent Alexander-Arnold.
The team for Saturday’s hard-fought win over the Swiss included debutants Marc Guehi, Kyle Walker-Peters and Tyrick Mitchell.
Their inclusion took England boss Southgate to the milestone of having used 100 players during his tenure, which began in 2016 and comprises 69 matches.
The proposed changes for Tuesday opens the door to the likes of Aston Villa pair Tyrone Mings and Oli Watkins, Southampton duo Fraser Forster and James Ward-Prowse, and Borussia Dortmund midfielder Jude Bellingham.
Forster – a late call-up in place of Ramsdale – could make his first England appearance since 2016.
There could also be a first start for Crystal Palace full-back Mitchell, who came off the bench for the final 30 minutes at the weekend.
“Whenever we bring players into the squad, it is great to see how they cope,” said Southgate.
“Sometimes, it isn’t about the opposition quality, although [against Switzerland] that was high. Sometimes, it is about the weight of an England shirt and whether they can cope.
“I thought all of the players who came in did really well. That was positive.
“I hope we have an environment where all the players feel comfortable and can be the best version of themselves in. A lot of that is down to the environment they have created.
“We have super characters; when younger players come in, the older ones are sitting with them at meal times, helping them feel relaxed and at ease.
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