The all-rounder aggravated a long-standing knee problem during last week's first Test.
It was initially thought that Stokes would only miss Friday's second Test at his home ground in Durham, but the 24-year-old has now revealed that he will also sit out the final meeting at Lord's on June 9.
"Devastated to be missing the rest of the series,this has been a ongoing issue for 2/3 years which I've managed to play through until now," he tweeted.
"All the best to the lads in the rest of the series, see you down at @DurhamCricket in the crowd."
Stokes is also expected to miss the upcoming limited-overs series, as well as being a doubt for the summer's Test clashes against Pakistan.