Arsenal defender Chambers was initially named in Gareth Southgate's Under-21 party for a Euro 2015 qualifying play-off against Croatia.
However, the 19-year-old, who claimed his maiden full international cap in last month's 1-0 victory over Norway, will now link up with Roy Hodgson's squad ahead of Euro 2016 qualifiers against San Marino and Estonia.
Stones' withdrawal comes as a result of the Everton man damaging ankle ligaments in Sunday's 2-1 defeat to Manchester United.
Everton boss Roberto Martinez confirmed after the game at Old Trafford that Stones would require further assessment.
A subsequent statement from the Football Association read: "Following John Stones' injury on Sunday afternoon, the Everton defender will not report to St George's Park for England duty on Monday.
"England manager Roy Hodgson has subsequently called up Calum Chambers, who was previously due to report to the Under-21s squad.
"Chambers will now be part of the senior squad for the Euro 2016 qualifying double header against San Marino and Estonia.
"England Under-21s manager Gareth Southgate is not calling any further players into his squad to face Croatia in their Euro 2015 play-off."
Hodgson's side face San Marino at Wembley on Thursday before taking on Estonia in Tallinn three days later.
