Woakes, who will be unavailable for the first part of the series with a right quad strain, joins Ben Stokes (left hamstring tear) on the injured list.
Both players have commenced their injury rehabilitation programmes and will be hoping to respond to treatment with the aim of featuring in the later stages of the series.
Both Woakes and Stokes will be unavailable to take on Scotland in Sunday's one-off one-day international and for the "first part" of the series against Australia.
Ball, 27, last played for England at the start of the year in Perth and was an integral member of the squad that defeated Australia 4-1 in the series Down Under.
The first ODI will be played on June 13 at The Oval before the action moves to Cardiff (June 16), Trent Bridge (June 19), Chester-le-Street (June 21) and the final at Manchester on June 24.
England ODI squad: Eoin Morgan (Captain), Moeen Ali, Jonny Bairstow (WK), Jake Ball, Sam Billings, Jos Buttler, Tom Curran, Alex Hales, Liam Plunkett, Adil Rashid, Joe Root, Jason Roy, Ben Stokes, David Willey, Chris Woakes, Mark Wood.
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