Test vice-captain Stokes was included in England's Ashes squad announced Wednesday, despite 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.
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 late on Sunday after playing alongside him during England's win over West Indies in the third one-day international in Bristol, has also been suspended from international selection.
"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.
"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."
Stokes's hand 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 the end of their home season.
Their next international match will be when they start their Ashes defence with the first Test against Australia in Brisbane commencing on November 23, although they do have three warm-up tour games prior to that fixture.
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