Stokes was alleged to have punched Ali, 28, in the fracas, but the England and Durham all-rounder argued that he had acted in self-defence.
But the jury returned a verdict of not guilty against the England cricketer and also cleared Ali of the same charge.
Mr Stokes, 27, has insisted he was acting in self-defence when he punched Ryan Ali, 28, and Ryan Hale, 27, near a nightclub in the Clifton Triangle area of Bristol in the early hours of 25 September past year.
Stokes's hearing for his involvement in a pub brawl that happened on September 24 after England's win over West Indies was taking place in the Bristol Crown Court.
Prosecutors wanted to charge Stokes with two counts of assault over the fracas near a nightclub past year in the southwest English city.
Prosecutors said all-rounder Stokes, who helped England to victory in the first test against India this month but missed the second match because of the trial, had lost control after drinking heavily earlier in the night. The two men shook hands after the jurors pronounced the verdict earlier today.
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Stokes said he heard best friends Ryan Ali and Ryan Hale direct homophobic abuse at William O'Connor and Kai Barry - but was unable to say what those words were.
"As soon as I see Mr Ali swing the bottle and physically hit them that's when I took the decision to get involved", Stokes said.
Ali, who is an emergency services worker, had drunk six or seven Jack Daniels and Cokes during his night out with former soldier Hale.
Ali recalled walking along the street with Hale, Barry and O'Connor, "having a laugh and some banter and the next thing I remember is having a tall blond man charging towards me".
Mr Barry added: "I thought he (Stokes) was just a normal lad, sticking up for someone who was obviously weaker than he was, which was quite nice".
He said that deciding to use a bottle as a weapon would be a "difficult decision for me to take".
Stokes will join up with the national team for the third test against India, which starts Saturday, the England and Wales Cricket Board said.