Stokes suffered a calf injury while bowling during England's 330-run win in the second Test at Old Trafford, a win that saw them level the four-match series at 1-1.
He was not considered for the third Test at Edgbaston, which started Wednesday, and officials have now confirmed he will take no part in next week's series finale at The Oval.
Stokes's latest injury means he won't complete a Test match in the 2016 English season after a knee injury cut short his participation in the series opener against Sri Lanka at Headingley in May.