Daniel Boylett, 36, of Eltham, south-east London, launched his attack on 25-year-old bird of prey Kayla during a clash at Selhurst Park in September 2015, Croydon Crown Court heard.
The third-round cup tie descended into violence and as Kayla's handler Chris Belsey walked her around the pitch on his forearm a punch was thrown from the crowd.
Boylett's lawyer claimed he had acted in self defence as he did not expect to see a bird of prey fly towards him.
Prosecutor Daniel Higgins previously told the court: "As he passed the stand he noticed three or four fans were shouting abuse and one of these three or four lent over the barrier and threw a punch directed at Kayla.
"Mr Belsey is unsure if the punch directed at the eagle had landed."
Mr Higgins said Kayla "seemed unhurt" but added "due to her delicate bone structure if she had been hit with force, her bones could easily break".
Boylett appeared in the dock alongside Colin Kitto, 49, of Eltham, Andy McConville, 48, of Rochester, Kent, Billy Cowcher, 32, of Greenwich, south east London, and Sam Donegan, 25, of Welling, Bexley, in south London, who had been charged with football violence.
A jury took four hours and 22 minutes to reach all its verdicts which stem from the ugly scenes which marred the Capital One third-round tie at Selhurst Park on September 23 2015.
Boylett was also found guilty of violent disorder.
Crystal Palace, who are nicknamed the Eagles, adopted Kayla as their mascot in 2010.
Charlton lost the match 4-1.
Mr Higgins said there "was disorder at the match before, during and after" the game.
Kitto was found guilty of violent disorder.
Donegan was cleared of violent disorder but found guilty of an alternative charge of affray.
Before the kick-off police had spotted a "distinct group" of about five or six fans who had met at a pub in Thornton Heath, south London, before the match, according to Mr Higgins.
Kitto, who was constantly on the phone, appeared to be organising this lead group, the court was told.
Kitto at one point was seen with a can in his hand.
The first scuffles broke out as police escorted the Charlton supporters to the ground.
Officers stood shoulder to shoulder as the crowd tried to push and break the police cordon to get to the rival fans.
One officer suffered a cut lip after being hit by what he thought was a bottle.
After the match, Donegan ran at a police cordon wielding a large yellow cone.
He ignored police shouts to stop and was subdued with a baton strike.
During his police interview, he said: "I was just annoyed, obviously.
"We just got battered. I just picked it up and let my anger out."
McConville was found not guilty of violent disorder.
The jury were directed to acquit Cowcher, Boylett, Kitto and McConville on a count of violent disorder due to insufficient evidence earlier this week.
Not guilty verdicts were recorded.
The defendants were released on bail to be sentenced on April 28.