Test vice-captain Stokes was included in England's Ashes squad announced Wednesday, despite reportedly injuring his hand in the incident that led to his arrest on suspicion of causing actual bodily harm.
The 26-year-old Durham all-rounder was released without charge on Monday but remains under investigation.
Authorities rake over Stokes's Ashes after brawl video emerges
The Sun newspaper published the footage from outside a nightclub in the southwest city of Bristol late on Wednesday.
Opening batsman Alex Hales, who was with Stokes on Sunday after playing alongside him during a win over West Indies in the third one-day international in Bristol, has also been suspended from England international selection.
"Ben Stokes and Alex Hales will not be considered for selection for England international matches until further notice," said an England and Wales Cricket Board statement.
"Each remains on full pay pending further ECB investigation and the ongoing police investigation into an incident in Bristol in the early hours of Monday 25 September.
Stokes given Ashes spot despite arrest
"Andrew Strauss, director of England cricket, will today refer the internal disciplinary procedure for these two players to the Cricket Discipline Commission, chaired by Tim O'Gorman."
The statement added: "These decisions, fully supported by ECB chairman Colin Graves, were made following the release of footage viewed by ECB for the first time on Wednesday night."
Neither Hales, who returned voluntarily to Bristol on Tuesday to give further evidence to police about the incident, nor Stokes were selected for Wednesday's six-run win over West Indies in the fourth one-day international at The Oval that gave England an unbeatable 3-0 series lead.
Stokes's finger injury may well have meant he was physically unfit for selection in any case.
England have one more international fixture — the fifth ODI against West Indies in Southampton on Friday — before they are due to travel to Australia on October 28.
Dawid Malan has been added as cover to the squad for the Southampton match after Hales was ruled out.
Ashes-holders England's next international fixture will be the first Test against Australia in Brisbane commencing on November 23.
Hales, who last played Test cricket over a year ago, was not included in the Ashes squad.
England suspend Test vice-captain Stokes
Meanwhile England coach Trevor Bayliss said Thursday that events of the past few days had been one of the toughest challenges of a career that saw the 54-year-old Australian caught up in a deadly 2009 terror attack on a team bus in Lahore while coaching Sri Lanka.
"It's right up — it's probably in the top two (in my career), I would have thought," said Bayliss. "It's very difficult for everyone involved.
"It's something that obviously we didn't want to go through, and hope we don't go through again," added Bayliss, who had previously spoken of his disappointment that Stokes had been out as late as 2:35 am (0135 GMT), when police were called to the incident, while defending the decision to retain the "cricket leader" as vice-captain of the Test side.
Stokes, potentially just one on-field offence away from a Test ban under the International Cricket Council's code of conduct, is seen as vital to England's chances of retaining the Ashes, with former England captain Michael Vaughan, saying: "I don't think England can win in Australia without Ben Stokes."
This is not the first time Stokes has been involved in a controversial off-field incident.
In 2011 he was arrested and later cautioned for obstructing police on a pre-Christmas night out.
And in February 2013 he was sent home from an England A team tour of Australia for flouting rules on late-night drinking.
In June last year Stokes was fined after he was caught speeding for a fourth time and warned a further offence could lead to a prison sentence.
Stokes told The Times in an interview published on Saturday he enjoyed a couple of beers after stumps.
"We're grown men, go out for dinner, have a few pints," he said. "I'm 26, not 14. I don't have to drink Diet Cokes with dinner."
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