Key all-rounder Stokes was not officially named on Tuesday morning in a 14-man squad which does contain the uncapped Sam Curran - who made his Test debut at Headingley this month.
England announced the previous day that the hamstring tear Stokes suffered before that Test against Pakistan was "progressing well", and it was hoped he may be able to play in the three-match Twenty20 series starting against India on July 3.
That option still appears possible, because the key all-rounder will travel with the squad chosen for those three matches and the one-off fixture against Australia which will follow the ongoing one-day international series - at Edgbaston on June 27.
Seamer Mark Wood is rested from the squad, with Jake Ball instead in the running to win his first Twenty20 cap, while there are a clutch of notable omissions.
Batsman Dawid Malan has made four half-centuries in just five Twenty20 appearances to date - including two in succession in England's most recent matches in New Zealand last winter. He averages exactly 50 in the format, with a strike rate above 150.
There is no place for him, however, along with short-format regulars Sam Billings and Liam Dawson - while Joe Root and Jonny Bairstow return alongside Moeen Ali, after the Yorkshire pair were rested from England's Twenty20 programme last winter.
The England and Wales Cricket Board attached a brief statement to the squad announcement.
It read: "Durham seamer Mark Wood is rested.
"All-rounder Ben Stokes will be with the squad throughout the series as he continues his rehabilitation from his torn left hamstring."
As expected, Chris Woakes is not yet fit after tearing his thigh and having an injection in a knee injury which England have described as "chronic".
He still hopes to be available again in time for the three-match ODI series against India, which starts on July 12.
England Twenty20 squad (v Australia and India): EJG Morgan (Captain), MM Ali, JM Bairstow, JT Ball, JC Buttler (wkt), SM Curran, TK Curran, AD Hales, CJ Jordan, LE Plunkett, AU Rashid, JE Root, JJ Roy, DJ Willey
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