Green experienced what Cricket Australia has described as "low grade side soreness" at training this week and was withdrawn from the squad on Friday.
The 26-year-old's injury has resulted in an ODI recall for Marnus Labuschagne, who was the biggest axing from the squad when it was initially named earlier this month.
Green underwent radical spinal surgery a year ago, and only recently returned to bowling duties.
He sent down four overs during Western Australia's Sheffield Shield loss to NSW earlier this month - his first competitive overs in a year - and said he was planning to be unrestricted by the start of the Ashes on November 21.
Green's side niggle could delay those plans, but Cricket Australia are confident the issue isn't serious.
"Green will complete a short period of rehabilitation and is tracking to return to play in round three of the Sheffield Shield to continue his preparation for the Ashes," Cricket Australia said in a statement.
Labuschagne will join up with the ODI squad following the completion of Queensland's Shield clash with South Australia in Adelaide.
The 31-year-old is favoured to win back his Test spot after producing four centuries from five innings to start the domestic season.
His latest heroics was a knock of 159 off 197 balls as Queensland posted a first-innings total of 398 against SA.
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