The ruling by a judge came on the second day of a trial stemming from a fight in August 2005 outside a restaurant near downtown Chicago.
"He was pretty happy about the outcome," Michael Higgins, Allen's agent, said. "I think this has been dragged out for too long. It's been a long time coming."
An earlier report by the Associated Press saying charges had been dismissed against Allen was incorrect. The AP reported Wednesday that the information came from Allen's agent.
Instead, the outcome was a not guilty decision from the judge.
Allen, who has spent the last three seasons with the Celtics, is recovering from two torn ligaments in his left knee sustained when he landed awkwardly after an uncontested dunk in the final minutes of a 97-84 loss to Indiana on Jan. 10.
Judge James Linn found Allen not guilty of the charges resulting from the fight in which one man was shot and another had his right eye socket fractured. The incident was recorded on a security camera at the restaurant, the White Palace Grill. Allen was accused of breaking the man's left eye socket. Police said he was not a suspect in the shooting of a man in the left arm and left side.
Two men, Nigel Odum and Marktwain Johnson, said the fight began when Allen punched Odum. They have brought a civil suit against Allen, which Higgins expects will be dismissed.
"After how quickly the judge ruled on this, that [suit] isn't going to go very far," Higgins said. "He's been the focus, I think, over the past couple of years of a couple of guys looking for him to take the fall."
Allen, the 25th pick in the 2004 draft out of Oklahoma State, grew up in Chicago. He was having his best season when he was hurt and finished with a scoring average of 11.5 points in 33 games.
The Associated Press contributed to this report.