Attorney Michael Norris entered the plea on behalf of the 21-year-old actor Wednesday, a day after a judge issued a $1,000 bench warrant for LaBeouf's arrest.
The bench warrant, which didn't contain details on the circumstances or the location of the offense, was dismissed.
A hearing was set for April 24. If convicted, the "Transformers" star faces a maximum penalty of a $1,000 fine and six months in jail.
LaBeouf was arrested in November for refusing to leave a Chicago drugstore, but prosecutors later dropped charges because Walgreen Co. and a security company indicated they didn't want to continue the case.
He starred on the Disney Channel show "Even Stevens" and can next be seen on the big screen opposite Harrison Ford in "Indiana Jones and the Kingdom of the Crystal Skull."