The 29-year-old was picked to start against Belgium on Tuesday night at Wembley but was forced off just 10 minutes into the match, with Joe Gomez replacing him and Ezri Konsa moving to centre-back.
Stones appeared to jar his leg after slightly slipping on the wet turf following a poor touch and he was unable to continue despite trying to run off the injury.
Southgate is unsure of the severity of Stones’ problem but says he has suffered an adductor injury, with the defender now a significant doubt for City’s clash with Arsenal.
Asked about the injury and whether it was a risk to play Stones, Southgate replied: ‘Well no, the first game [against Brazil] for him wasn’t a game that was high level in terms of the intensity.
‘We’ve done exactly what Holland did with Virgil van Dijk tonight, what Norway did with Erling Haaland and Martin Odegaard, starting them again.
‘Holland also started Nathan Ake again. So it only ever seems to fall on us when there’s a question about that.
‘But of course we’re disappointed if he’s got a problem. It seems to be in the adductor area. We’ll just have to see.
‘John also came in on the back of not having played for two weeks so it wasn’t an overload situation. But I hate sending players back to their clubs if they’re not fully fit, of course.’
The news is a blow for Pep Guardiola ahead of Sunday’s clash against Arsenal, with City already sweating over the fitness of Kyle Walker – who limped out of Saturday’s loss to Brazil – and Manuel Akanji.
Southgate was without a host of key, senior players for this month’s friendlies and he says his final plans – and squad – for the Euros will be hugely dependent on who makes it through the rest of the season unscathed.
‘We’ve got so many players missing at the moment and we’ve still got the heat of the season to come,’ the England boss added.
‘We’re not going to know what we’re left with until right at the very end and we’ll have to make the best decisions.’
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