The 20-year-old Grammy-nominated singer was not present for the arraignment at Superior Court in Van Nuys. Bieber's lawyer, Shawn Holley, entered the plea on his behalf.
A spokeswoman for Bieber said he's glad to have the matter resolved and behind him. She added that he will move forward and focus on his career and music.
A hearing to check on Bieber's progress toward completing his sentence was scheduled for Aug. 12.
Prosecutors spent months deciding whether to file charges after the January incident. They considered felony charges because the damage was said to be more than $400, the threshold for a felony.
Deputy District Attorney Alan Yochelson said Wednesday he was satisfied with the misdemeanor charge and called egg throwing an "extremely immature and a silly act."
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The singer's Calabasas mansion was searched Jan. 14 and detectives later filed a search warrant to obtain images from Bieber's Instagram account to match them to surveillance footage taken from his home. A detective wrote that a person matching Bieber's description was seen high-fiving his friends after running toward a neighbor's home, but footage of the egg attack was not captured.
Bieber was not arrested during the search of his home, but his friend and personal manager Xavier Domonique Smith was charged with felony drug possession. Smith, an aspiring rapper who goes by the name Lil Za, pleaded no contest to felony possession of Ecstasy and was sentenced to probation and a drug treatment program.
Bieber has since moved from Calabasas into a Beverly Hills condominium.
The singer faces two other cases in Florida and Toronto. A Miami court has set a trial date this month for his DUI case, which also includes charges that he resisted arrest without violence and was driving with an expired license.
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A preliminary toxicology report showed that the singer tested positive for marijuana and the anti-anxiety drug Xanax after his arrest, but no other illicit drugs were found in his system.
The singer turned himself in to Toronto authorities Jan. 29 on a charge that he assaulted a limo driver in late December. Another of Bieber's attorneys, Howard Weitzman, has said that Bieber is innocent in that case, which he described as being the equivalent of a misdemeanor case in the U.S.
Bieber gained stardom with his debut album at age 15 and his career has been guided by a pair of music industry heavyweights, singer Usher and manager Scooter Braun. He has been nominated for two Grammy Awards for his 2010 full-length album debut "My World 2.0," but his popularity has waned.