Magistrate Belinda Wallington dismissed some of the charges that had been heard in the four-week preliminary hearing in Melbourne, but decided the prosecution's case against Pell was strong enough to warrant a trial by jury.
When she asked the cardinal how he pleaded, he said in a firm voice: "Not guilty."
Lawyers for Australia's highest-ranking Catholic had argued the accusations were untrue and should be dismissed.
Pell, Pope Francis' former finance minister, was charged last June with sexually abusing multiple people in his Australian home state of Victoria.
The details of the allegations against the 76-year-old have yet to be released to the public, although police have described the charges as "historical" sexual assault offences.
His alleged victims testified in the first two weeks of the preliminary hearing via a video link from a remote location to a room closed to the media and public.
His lawyer Robert Richter told Wallington in his final submissions two weeks ago that the complainants might have testified against one of the church's most powerful men to punish him for failing to act against abuse by clerics.
But prosecutor Mark Gibson told the magistrate there was no evidence to back Richter's theory that Pell had been targeted over the church's failings.
Since Pell returned to Australia from the Vatican in July, he has lived in Sydney and flown to Melbourne for his court hearings. His circumstances are far removed from the years he spent as the high-profile and polarising archbishop of Melbourne and later Sydney before his promotion to Rome in 2014.
The case places both the cardinal and the pope in potentially perilous territory. For Pell, the charges are a threat to his freedom, his reputation and his career. For Francis, they are a threat to his credibility, given he famously promised a "zero tolerance" policy for sex abuse in the church.
So far, Pope Francis has withheld judgment of Pell, saying he wants to wait for justice to run its course. And he did not force the cardinal to resign, although Pell took an immediate leave of absence so he could return to Australia to fight the charges. Pell has said he intends to continue his work as a prefect of the church's economy ministry once the case is resolved.
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