Woakes has been ruled out until mid-July with a right quad tear, while Stokes could recover from a torn hamstring in time for England's Twenty20 series with India.
Fast bowler Woakes's chronic knee problem is thought to have flared up his current tear, which he suffered in the second Test against Pakistan at Headingley earlier this month.
The 29-year-old had an injection in his ankle last Monday and will now undertake a rehabilitation programme to address both issues.
All-rounder Stokes, meanwhile, has been cleared to return to bowling two weeks after tearing his hamstring following the first Test against Pakistan.
The 27-year-old has returned to batting and could feature for England against India, with the series beginning on July 3.
England are 2-0 up in their five-match one-day series with Australia, with the third tie to be played on Tuesday.