Woakes suffered a right quad strain during the latter stages of England's victory over Pakistan in the second Test at Headingley last week, and will be unavailable for the first part of the series.
He had been recalled to the Test side in Leeds having been left out of the opening Test at Lord's when England preferred Mark Wood. He claimed 3 for 55 in the first innings and then removed Sarfraz Ahmed in the second before reporting discomfort.
Woakes is the second of England's allrounders to suffer injury ahead of the Australia visit, after Ben Stokes was forced to sit out the Headingley Test with a left hamstring tear. Both players have commenced their injury rehab programmes and remain hopeful of featuring in the latter stages of the five-match and one T20I series against Australia which commences at The Oval next Wednesday.
Ball, 27, played the most recent of his 17 ODIs at Perth in January, where he did not take a wicket but contributed to a 12-run win that sealed an impressive 4-1 series win against Australia.
Tom Curran, whose brother Sam made his Test debut at Headingley, had already been named in the squad to face Australia, but was called up as cover for Woakes for Sunday's one-off ODI against Scotland as well.
Several members of England's Test squad, including some dual-format players, will be in action for their counties this week in the Royal London Cup, as they switch their attention from red-ball to white.
Joe Root, England's Test captain, is available for Yorkshire's home game against Northamptonshire on Thursday; a match that could yet decide which teams qualify for the knock-out stages.
Other players from England's Test squad available for Royal London Cup fixtures this week are Dom Bess (Somerset), Mark Wood (Durham), Keaton Jennings (Lancashire), Dawid Malan (Middlesex) and Sam Curran (Surrey). Malan has also been made available to play for Middlesex in their County Championship match against Leicestershire starting on June 20.
Jonny Bairstow and Jos Buttler have been rested ahead of the ODIs, while England are yet to make a decision on the county availability of James Anderson and Stuart Broad ahead of the start of the Test series against India in August. They have, however, confirmed that neither will be available for the next round of County Championship matches which starts on Saturday.
But Alastair Cook is available for Essex's Championship game against Lancashire and Moeen Ali will play for Worcestershire's final Royal London game before joining up with England's limited-overs squad.