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Root, the Ashes player of the series after his 460 runs played a central role in England's 3-2 win over the five Tests, has been a key player in all three international formats in recent times.
But with England facing tough Test series away to Pakistan and South Africa later this year, England's selectors have decided to give the 24-year-old a break from international duty.
Also omitted are senior bowlers James Anderson, currently out with a side strain, and Stuart Broad, whose stunning eight for 15 at his Trent Bridge home ground saw Australia skittled out for 60 in the third Ashes Test.
Neither Anderson nor Broad, as well as veteran batsman Ian Bell, have played a 50-over one-day international since this year's World Cup, which Australia won on home soil in March.
Test skipper Alastair Cook, dropped from England's squad before the global showpiece, was again omitted from white-ball duty.
Eoin Morgan will again captain both squads, having led England in their miserable first-round exit from the World Cup before overseeing a thrilling one-day series win at home to World Cup finalists New Zealand.
Essex left-arm seamer Reece Topley was the only uncapped player in either squad after being named in the Twenty20 party.
Moeen Ali was restored to both squads after being injured at the start of the season, with fit-again fellow all-rounder Chris Woakes also selected.
But there was no place for Yorkshire wicketkeeper batsman Jonny Bairstow even though he revived his international career with a series-clinching 83 not out against New Zealand at Chester-le-Street in June.
"We have made some significant progress in our limited-overs cricket this summer, and the next six games allow these players to continue testing themselves against one of the very best sides in the world," said England national selector James Whitaker.
"This is primarily a young group of players, and the next three weeks will provide them with valuable experience as we continue to identify those who can take our limited-overs cricket forward over the next four years."
Yorkshire paceman Liam Plunkett, included in the ODI squad after spending much of this season as cover for England's Test bowlers, was well aware of the challenge posed by Australia.
"They won the World Cup not so long ago - they are the best in the world, so it's going to be a tough 'ask'," said Plunkett.
"But we beat New Zealand, who were in that World Cup final, so it shows where we are - and I am really looking forward to the tough competition."
The lone Twenty20 clash takes place in Cardiff on August 31, with the one-day series starting at Hampshire's Ageas Bowl headquarters on September 3.
Australia face Ireland in a one-day international in Belfast on Thursday in what will be their first 50 overs per side clash since the World Cup.
With former captain Michael Clarke having retired from international cricket after the Ashes, the upcoming white-ball games will mark Steven Smith's first campaign as the full-time one-day skipper of Australia.
England T20 squad
Eoin Morgan (Middlesex, captain), Moeen Ali (Worcestershire), Sam Billings (Kent), Jos Buttler (Lancashire, wkt), Steven Finn (Middlesex), Alex Hales (Nottinghamshire), Adil Rashid (Yorkshire), Jason Roy (Surrey), Ben Stokes (Durham), Reece Topley (Essex), James Vince (Hampshire), David Willey (Northamptonshire), Chris Woakes (Warwickshire)
England ODI squad
Eoin Morgan (Middlesex, captain), Moeen Ali (Worcestershire), Sam Billings (Kent), Jos Buttler (Lancashire, wkt), Steven Finn (Middlesex), Alex Hales, (Nottinghamshire), Liam Plunkett (Yorkshire), Adil Rashid (Yorkshire), Jason Roy (Surrey), Ben Stokes (Durham), James Taylor (Nottinghamshire), David Willey (Northamptonshire), Chris Woakes (Warwickshire), Mark Wood (Durham)
Fixtures
August 31: Twenty20, Cardiff
September 3: 1st ODI, Southampton (D/N)
September 5: 2nd ODI, Lord's
September 8: 3rd ODI, Old Trafford (D/N)
September 11: 4th ODI, Headingley
September 13: 5th ODI, Old Trafford
