Stokes was arrested on suspicion of actual bodily harm after an incident outside a Bristol nightclub in September.
He has still been awarded a central contract, while pace bowler Steven Finn has been added to the tour party.
Jonny Bairstow, Jake Ball and Liam Plunkett have each been given written warnings for their conduct.
They are not connected to the Stokes incident, for which batsman Alex Hales volunteered to help police with their investigation.
All-rounder Stokes was arrested on a night out that followed England's victory over West Indies in the third one-day international.
Stokes and Hales were left out of the fourth ODI, but the 26-year-old was still named in the original Ashes squad.
After the touring party was named, the Sun newspaper published footage that allegedly showed Stokes involved in a street brawl.
The ECB then said that Stokes, who suffered a broken hand, and Hales would not be available to play for England until further notice, a stance it reiterated on Friday.
England leave for the five-Test series on 28 October.
England director of cricket Andrew Strauss said: "We have spoken to Ben and assured him that our decision in no way prejudges the outcome of the ongoing police investigation or cricket discipline commission process, as can be seen by the award of central contracts."
Finn's addition to the Ashes squad comes on the day that he loses his central contract, with fellow pace bowler Mark Wood losing his Test deal but gaining a white-ball contract.
Only eight players are awarded Test contracts, a reflection of England's uncertainty around their best XI in the longest form of the game.
Limited-overs specialist Hales is also included in the white-ball list and is joined for the first time by pace bowler Ball and wicketkeeper Bairstow.
Yorkshire batsman Gary Ballance loses his incremental deal, but fast bowler Toby Roland-Jones is rewarded after his breakthrough international summer.
Central contracts give the ECB control over a player's schedule, with the governing body picking up the majority of his salary.
Previously, they mainly focussed on Test players, but were revamped in 2016 to give greater recognition to limited-overs specialists.
Test captain Joe Root, Moeen Ali, Bairstow and Stokes are the only players to receive both a Test and white-ball contract.
"With the Ashes just around the corner, it's important to give the players, the coaching staff and supporters some clarity around a complex situation," said Strauss.
"This decision will help us in the weeks ahead and gives every player and the whole England set-up the best chance to focus on the challenge ahead in Australia.
"Steven is a high-quality cricketer, with considerable experience of both international cricket and Australian conditions. The selectors believe he will add to the range of options and the squad will be further supported by the arrival of the Lions in Australia in November."
There had been no suggestion of any wrongdoing by Ball, Bairstow or Plunkett until the ECB revealed the issue of the written warnings.
All three players have paid an undisclosed sum to to the Professional Cricketers' Association Benevolent Fund and the Hornsby Professional Cricketers' Fund.
The ECB said that the internal investigation into that matter had been closed and that it will make no further comment.
Speaking before the warnings were issued to Ball, Bairstow and Plunkett, former captain Michael Vaughan said that the Stokes incident highlighted a cultural problem with the England team.
"Yes, Stokes is 26 years of age, he should be more mature, he has made a massive mistake and I have no sympathy for him whatsoever," Vaughan told BBC Radio 5 live.
"But the management of the England team have to look at themselves in the mirror and say, 'Hang on a minute, could we have done a bit more, could we have been a bit stricter?'.
"I am not saying I want a headmaster and have a curfew and say ,'You have got to be in your room by 11pm and you can never drink', but there is a time and a place and I just think now, with what has gone on this week, the culture of cricket has to change quickly."
Centrally contracted players for 2017-18
Test contracts: Moeen Ali, James Anderson, Jonny Bairstow, Stuart Broad, Alastair Cook, Joe Root, Ben Stokes, Chris Woakes.
ODI/T20 contracts: Moeen Ali, Jake Ball, Jonny Bairstow, Jos Buttler, Alex Hales, Eoin Morgan, Liam Plunkett, Joe Root, Adil Rashid, Jason Roy, Ben Stokes, David Willey, Chris Woakes, Mark Wood.
Incremental contract: Toby Roland-Jones.