Several observers reported that Stokes shook Mr Ali's hand after the verdicts were delivered.
A Cricket Discipline Commission investigation into the behaviour of Stokes and team-mate Alex Hales was put on hold while court proceedings took precedence.
Stokes, 27, was accused of knocking unconscious two men, Ryan Ali and Ryan Hale, in a brawl in Bristol, southwest England, last September just hours after he had played in a one-day worldwide against the West Indies.
Stokes missed the second Test at Lord's this week due to his appearance at Bristol Crown Court.
The prosecutors alleged that Stokes abused the doorman of a nightclub in Bristol after the latter denied the cricketer re-entry.
During the trial, the court was told that Stokes lost control after drinking heavily. The jury is likely to retire overnight to consider their verdict in a case that involves one other co-defendant, Ryan Ali.
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He said Stokes was mimicking the mannerisms and voices of two gay men, William O'Connor and Kai Barry, outside the club but the cricketer insisted they were exchanging "banter" about his expensive white leather shoes.
He said he had not been drunk but admitted he could not remember what the had been said. Hale was acquitted of the same charge part way through the trial at Bristol Crown Court.
Mr Ali, an emergency services worker, told jurors the England cricketer "was very angry and looking for someone to pick on" and said he only used a bottle after what would have been a "difficult decision for me to take".
A bouncer had claimed that he witnessed Stokes mock Mr O'Connor and Mr Barry, but they later told ITV News that they were grateful to Stokes for his intervention.
"I didn't know, they could be carrying more weapons on them".
"I just didn't want any trouble so I was backing away, trying to retreat".
Stokes has been left out of England's 13-man squad for the third cricket test against India.