In a triumph for victims of clergy sex abuse nationwide, a Santa Clara County jury on Thursday acquitted a San Francisco man of felony assault and elder abuse for beating up the cleric he says brutally raped him as a child decades ago.

Reflecting the powerful emotions that Will Lynch provoked throughout the nationally watched, three-week proceeding, the jury also failed to convict him of the lesser charges, even though Lynch admitted on the stand that he pummeled the Rev. Jerold Lindner two years ago at a Jesuit retirement center in Los Gatos. The panel acquitted him of misdemeanor elder abuse. On the charge of misdemeanor assault, four jurors refused to agree that Lynch was guilty, leading to a mistrial on that count.

The verdict thrilled Lynch’s many supporters, who faithfully packed the San Jose courtroom during the three-week trial and picketed outside bearing signs that read, “Jail Father Jerry, “Sacred Heart Jesuit Center: Pedophile Playground” and “Help Free Willy.”

And it seemed to bring Lynch a strong measure of redemption at the conclusion of his high-risk legal strategy. Lynch had set out to bring Lindner to the judgment he never received because a short legal statute of limitations prevented the priest’s prosecution. In the end, Lindner’s actions became as much the focus of the trial as Lynch’s attack.

“I was wrong for doing what I did — in doing that I perpetuated the cycle of violence,” Lynch said outside the courtroom. “But if there is anything I want people (who have been molested) to take away from this — it is you can come forward, you can seek justice and you can find justice in many forms.”

Not only was Lynch acquitted of the felonies and one of the two misdemeanors, but he also drew national attention to the anguish of clergy sex-abuse survivors and publicly pilloried Lindner, who briefly took the stand in the trial to deny abusing Lynch before invoking his right not to incriminate himself. The judge told jurors to disregard Lindner’s appearance, putting the focus back on Lynch’s emotional plight.

Tears streaming down her face, Lynch’s mother Peggy mouthed “thank you” to the three women and nine men on the jury. Lynch, who had expected to be convicted of at least a misdemeanor, embraced his attorneys.

“My heart leaped, ” said Will Lynch’s younger sister, Amanda Lynch, of her reaction when the clerk read the jury’s decision.

The verdict was a sharp blow to prosecutors, who argued that although they believed that Lindner molested Lynch and his 4-year-old brother in the mid-1970s on a camping trip in the Santa Cruz Mountains, his repugnant act didn’t justify Lynch’s “vigilante” attack. The May 10, 2010, beating left the priest bruised and bloodied, with two cuts to his face and ear.

District Attorney Jeff Rosen left open the possibility of retrying Lynch on the misdemeanor assault charge, though some legal experts said it was unlikely.

“A just punishment is delivered through our justice system, not through the acts of one traumatized and troubled man,” said Rosen, outside the courthouse.

Asked if the trial was a waste of resources, Rosen responded, “You can’t put a price on justice.”

Defense attorneys called on the DA’s office to try Lindner for perjury for denying on the stand that sexual abuse had occurred. The DA’s office is reviewing the issue.

But Lynch’s attorneys had essentially argued prosecutors put the wrong man on trial.

“The D.A. says no man is above the law, but there is one man who has been above the law, who sits in a vineyard, with medical care and cars,” defense lawyer Pat Harris had said, referring to Lindner.

In a statement released after the verdict, the main victims group in the United States, Survivors Network of those Abused by Priests, thanked the jury.

Lynch said he plans to start a nonprofit organization to help other victims and lobby for the elimination of the statute of limitations for child molestation.

During the trial, the prosecution twice showed the jury a videotape of an exclusive interview Lynch gave to this newspaper, in which he gave a heartbreaking account of the alleged molestation and his emotional scars. Lynch also testified about being sexually assaulted and admitted hitting Lindner at least twice.

One juror called the rape of Lynch and his brother “heinous, absolutely heinous.”

Despite the judge’s admonitions, “(the alleged assault) was a tough thing to disregard, ” said the juror, a retired Silicon Valley accountant. “It played a big role in our decision.”

The juror was one of the eight who voted to convict Lynch for misdemeanor assault. Lindner testified last month about what he called a “vicious” and painful attack, but the juror said his account was not a factor in their vote. Judge David A. Cena had instructed the jury to ignore Lindner’s testimony, including his denial of the alleged molestation, after the Jesuit refused to answer any more questions on the grounds it might incriminate him.

The juror said after the priest’s testimony was thrown out and the testimony of the prosecution’s two eyewitnesses was disputed, “we all thought it would be not guilty. But then the defendant said he did it.”

The verdict capped off a tumultuous trial roiled by disruptions, from accusations of prosecutorial misconduct to an angry confrontation in the hallway between the priest and a woman, who claims he also sexually molested her.

Lynch’s lawyers called on prosecutors to charge the priest with perjury. But legal sources said they can’t because the judge struck Lindner’s testimony, wiping it off the record as if it never existed.

Lynch was charged with two felonies that together carried a maximum sentence of four years — assault by means of force likely to produce great bodily injury and elder abuse under circumstances likely to produce great bodily harm or death.

The jury also had the option of finding Lynch guilty of simple assault and a less serious form of elder abuse — both of which are misdemeanors punishable by up to a year in jail.

In 1998, the Jesuits paid Lynch and his brother about $187,000 each after legal fees to settle a lawsuit they filed claiming Lindner had raped Lynch and made him have oral sex with his 4-year-old brother. The order also paid another camper more than $1.5 million to settle her lawsuit. In 2007, one of Lindner’s nieces sued the Jesuits for Lindner’s alleged sexual abuse of her as a child and settled for $786,000.

But the molestation and lack of prosecution continued to eat away at Lynch. He testified he confronted Lindner in hopes he would sign a confession to sexually molesting him and his brother on the camping trip organized by a religious group.

He said he began pummeling Lindner after the priest refused to sign the confession and “leered” at him the same way he did during the alleged molestation decades ago.

In her closing argument, prosecutor Vicki Gemetti acknowledged the sympathy Lynch evoked, but she told jurors, “Two wrongs don’t make a right.”

Pat Harris, Lynch’s lead attorney, said the prosecution had a choice, but decided to “overcharge the case” by filing felonies stemming from an incident in which “the damage was less than a 10-second bar fight.”

In a sign earlier this week that at least some members of the jury were leaning toward acquittal, the panel took the highly unusual step of asking the judge for the definition of nullification, which is when a jury acquits a defendant despite evidence of guilt because it believes a conviction would be unjust.

The question initially stunned the judge and lawyers, who argued over how to respond. Over the vehement objections of Lynch’s lawyers, the judge ended up telling the jury today they had to obey his instrutions to follow the law, and deliberations continued. At that point, the defense braced for a conviction, said Paul A. Mones, one of Lynch’s attorneys.

Defense lawyers in California can’t directly urge the jury to nullify, But during closing arguments Harris had managed to get his message across.

“There is a defense to that “overzealous” decision by the prosecution, Harris had said — “you,” looking at the jurors.

Contact Tracey Kaplan at 408-278-3482.