Woakes, who sustained a right quad strain during last week's series-levelling test win over Pakistan, was already ruled out of the one-off ODI against Scotland on June 10.
The 29-year-old joins Ben Stokes on the sidelines as the latter recovers from a hamstring tear.
"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 England and Wales Cricket Board (ECB) said on Tuesday.
Ball last played for England in their 4-1 ODI series win at Australia in January.
England host Australia in five one-day matches starting at The Oval on June 13.
First Published: June 5, 2018, 3:55 PM IST