Everton's Stones, who sat out Sunday's Merseyside Derby against Liverpool with a knee injury, will miss the games against Estonia at Wembley on Friday and in Lithuania on Monday.
England are already guaranteed top spot in Group E and will finish the qualifying competition with a 100 percent record if they win their remaining two games.
Tottenham Hotspur right back Kyle Walker and winger Andros Townsend have been called into Roy Hodgson's squad for the double header with injury doubts also hanging over forwards Wayne Rooney and Danny Ings plus midfielder Jonjo Shelvey.
"Captain Wayne Rooney, first-time call-up Danny Ings and midfielder Jonjo Shelvey did not train after picking up knocks for their clubs at the weekend," said the FA.
"They will be monitored ahead of Friday's meeting with the Estonians at Wembley..."
Spurs winger Townsend last played for England against Slovenia in June, while Walker won his 11th cap in a friendly against Italy in March.
(Reporting by Toby Davis; Editing by Ken Ferris)
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