After playing the full 90 minutes for the Three Lions in last weekend's 1-0 defeat to Brazil, Stones was handed another start in central defence, this time partnering Lewis Dunk.
However, Stones's 71st international appearance lasted for just 10 minutes as he signalled to be withdrawn after jarring his leg when attempting to retrieve the ball.
The 29-year-old briefly required treatment on the pitch before limping down the tunnel, with Liverpool's Joe Gomez brought on as his replacement.
England conceded the opening goal just moments after Stones was taken off, with Belgium's Youri Tielemans netting either side of an Ivan Toney penalty, before Jude Bellingham rescued a draw for the Three Lions with a 95th-minute equaliser.
John Stones emerges as injury doubt for Arsenal clashStones is the latest Man City star to emerge as an injury doubt ahead of the Citizens' Premier League title showdown with leaders Arsenal at the Etihad Stadium on Sunday.
England teammate Kyle Walker lasted just 19 minutes in the Three Lions' loss to Brazil after tweaking his hamstring, although Man City are hopeful he will recover in time to face the Gunners.
Earlier on Tuesday, Manuel Akanji was forced to withdraw from the Switzerland squad after their head coach Murat Yakin revealed that the defender had picked up a knock.
Meanwhile, Matheus Nunes was not involved in Portugal's friendly defeat to Slovenia, with Portuguese news outlet B24PT, via @City_Xtra on 'X', claiming that the midfielder required treatment to a knock in his foot.
Kevin De
Read on sportsmole.co.uk