The all-rounder had originally been named in a 16-man squad despite being currently unavailable for international selection following his arrest in September.
And while he remains suspended on full pay, the ECB board are unwilling to play him until his situation is fully resolved.
Stokes is still waiting to find out if he will be charged with causing actual bodily harm following the late-night fracas outside a Bristol nightclub on September 25.
England are ready to grant a No Objection Certificate (NOC) for the all-rounder to play in the Indian Premier League.
But with both Cricket Australia and several influential ECB board members uncomfortable with the prospect of him representing England in Australia, the plug has been pulled on any possible participation in the ODI series.
The ECB is also expected to name a Twenty20 squad for next month’s Tri-Series against Australia and New Zealand in the coming days.