Avon and Somerset Police officers were called to a “disorder” in the Clifton Triangle area of Bristol at about 2.35am on Monday.
The 26-year-old all-rounder was arrested on suspicion of causing actual bodily harm and later released under investigation.
A 27-year-old man had suffered facial injuries and taken to the Bristol Royal Infirmary for treatment.
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Stokes’ England team-mate Alex Hales voluntarily returned to Bristol to help police with their inquiries, the England and Wales Cricket Board (ECB) said.
Both will miss the fourth Royal London Series one-day international against West Indies at The Oval on Wednesday.
Police have appealed for any witnesses to come forward.
The Clifton Triangle area, which has a number of bars, nightclubs and restaurants, is popular with students and people on a night out.
It is understood that the alleged incident took place in the street near a bar in Triangle West.
People who live above the bar said they did not hear police sirens in the early hours of Monday.
In a statement, the ECB said: “Ben Stokes and Alex Hales will not be available for tomorrow’s one-day international match against West Indies at The Oval.
“Stokes was arrested in the early hours of Monday morning, 25 September, following an incident in Bristol.
“He was held overnight and released under investigation - without charge - late on Monday and will not join the team in London.
“Hales, who was with Stokes on Sunday night, did not train this morning and has returned voluntarily to Bristol today to help police with their inquiries.
“You will understand that we cannot offer further detail at this stage but will provide any updates when we can.”
ECB director Andrew Strauss made an unexpected trip to The Oval to explain the reasons for Stokes’ and Hales’ absence.
Plans remain for England to name their Ashes squad before Wednesday’s match.
Stokes is a certain inclusion, as long as he is fit, but Hales is a less likely contender - having played the last of his 11 Tests 13 months ago.
In 2011, Stokes was cautioned after being arrested for obstructing police on a night out.
The following year, he was sent home from an England Lions tour in Australia, alongside team-mate Matt Coles, for repeatedly flouting rules on late-night drinking.
England were made to do without the all-rounder at the 2014 World T20 after he punched a dressing-room locker in Barbados, breaking his hand.
He appeared at Northallerton Magistrates’ Court in 2016, having been convicted of speeding for a fourth time.