The pair will miss the fixtures against Montenegro and Kosovo, it was announced on Sunday.
Sheffield United goalkeeper Dean Henderson – on loan from Premier League side Manchester United – will replace Aston Villa’s Heaton.
However, there is no replacement for England and Chelsea midfielder Barkley in Gareth Southgate’s squad.
England are three points clear at the top of Group A as they prepare to host Montenegro on Thursday before travelling to Kosovo on November 17.
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