LaBeouf is facing two counts of disorderly conduct and one count of criminal trespassing, said Brian Sessa, a police spokesman.
"It's due to his violent behavior toward patrons," he said.
It is unclear how long LaBeouf will be jailed.
People who attended the performance at Studio 54 said on Twitter that he was being highly disruptive.
"Just saw Shia LaBeouf in handcuffs in tears surrounded by 6 police officers outside of CABARET the musical. Oh New York, u is a crazy bitch," actor Benj Pasek said in tweet that has since been deleted.
"He was disruptive during Act 1 and escorted out of Studio 54 at intermission," a "Cabaret" representative said.
LaBeouf, who stars with Brad Pitt in the upcoming war drama "Fury," has exhibited particularly unusual behavior in recent months.
In December, the "Transformers" star found himself at the center of plagiarism allegations after he made a short film that bore remarkable similarities to a graphic novella by Daniel Clowes but did not credit Clowes.
In January, the actor announced that he was retiring from public life. The next month, he showed up at a movie premiere in Berlin wearing a paper bag over his head that read, "I am not famous anymore."
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