Woakes joined Ben Stokes on the injury list after suffering a thigh strain in England's thumping victory over Pakistan in the second Test at Headingley that ended on Sunday.
Both will be unavailable for this weekend's one-off one-day international against Scotland and, according to an England and Wales Cricket Board statement, the "first part" of the five-match series against Australia.
Ball is back after playing the last of his 17 ODIs in Perth in January in the 4-1 series victory over Australia. He has taken 21 wickets, with a best of five for 51, but averages 45.28.
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"Both players have commenced their injury rehab programmes and will be hoping to respond to treatment with the aim of featuring in the latter stages of the series," the ECB statement said.
The series starts at The Oval on June 13.
England squad:
Eoin Morgan (capt), Moeen Ali, Jonny Bairstow, Jake Ball, Sam Billings, Jos Buttler, Tom Curran, Alex Hales, Liam Plunkett, Adil Rashid, Joe Root, Jason Roy, David Willey, Mark Wood.
* Woakes and Stokes remain part of the squad too, but will both miss the start of the series because of their injuries.
