A Manhattan jury on Tuesday convicted ex-bodega clerk Pedro Hernandez of murder and kidnapping in 6-year-old Etan Patz’ 1979 disappearance, writing a final chapter in a notorious mystery that transfixed New Yorkers for 37 years and turned missing children into a national cause celebre.

The verdict on the ninth day of deliberations came two years after the first trial of Hernandez, 55, of Maple Shade, New Jersey, ended with a jury hung 11-1 for conviction, and was quickly lauded by a relieved Stanley Patz, Etan’s father, who appeared near tears as he heard the foreman say “Guilty.”

“The Patz family has waited a long time, but we finally have come to some measure of justice for our wonderful little boy, Etan,” Patz told reporters after sharing a long round of hugs, backslaps and tears with prosecutors and jurors from the first trial who had attended the retrial with him.

Members of the new jury said there were divisions — they declined to specify the breakdown — but eventually the panel was swayed by Hernandez’s confessions to police and friends, and dismissed defense claims that he was delusional when he said he lured Etan into the basement of the SoHo grocery where he worked before strangling the boy.

“Deliberations were difficult, but we had constructive conversations . . . that were analytical and creative and adaptive and compassionate, and ultimately kind of heartbreaking,” said Thomas Hoscheid, an engineer who was the foreman of the panel of eight men and four women.

Manhattan District Attorney Cyrus Vance Jr., traveling when the verdict was handed down, said in a statement: “Etan’s legacy will endure through his family’s long history of advocacy on behalf of missing children. . . . It is my hope that today’s verdict provides the Patz family with the closure they so desperately deserve.”

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In Brooklyn, Mayor Bill de Blasio told reporters that he remembered the “shocking moment” when Etan vanished without a trace in 1979 and hoped the verdict would give the city closure.

“People have felt the loss of this child for a long, long time,” he said.

The jury found Hernandez not guilty of second-degree intentional murder — jurors said they were not all convinced beyond a reasonable doubt of prosecution claims that he killed Etan after the boy resisted a sexual assault — but convicted him of kidnapping and second-degree felony murder, which includes even unintentional deaths that occur during the commission of another felony.

Hernandez’s wife and daughter, who both attended the trial regularly, were not present when the verdict came. Hernandez was impassive in court, but defense lawyer Harvey Fishbein said his client — who will face a potential prison term of life at his Feb. 28 sentencing — was unhappy with the outcome, and an appeal was a certainty.

“We are confident we’ll be back here,” Fishbein said. “Unfortunately we don’t think this will be the end of the story.”

Etan disappeared in May 1979 on his way to catch a school bus that stopped outside the corner bodega in SoHo where Hernandez worked. His mother, Julie, in emotional testimony, said it was the first time he walked to the bus stop alone, and he had $1 to buy a treat at the bodega.

Etan never came home and an intense police dragnet in the neighborhood failed to turn up a body, forensic evidence of a crime, or witnesses who recalled seeing him at the bus stop. The case became a cautionary tale for parents, and Etan’s picture was put on milk cartons as part of a nascent national campaign to find missing children.

In the 1980s, suspicion focused on Jose Ramos, a convicted child molester now serving time in Pennsylvania who had a relationship with a woman who once walked Etan home from school. Although Ramos intrigued authorities by telling them that he had an encounter with a boy who could have been Etan on the day he vanished, he never confessed and was never prosecuted.

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Hernandez was identified as a suspect by a relative in 2012. After a lengthy unrecorded interrogation by the NYPD in 2012, he recorded purported confessions for police and prosecutors that were the centerpiece of the case against him.

According to testimony at trial, he had also made incriminating statements that varied in the details to a prayer group, an ex-wife, and a friend, long before he was identified and picked up by police.

But the defense said he suffered from schizotypal personality disorder, a mental problem that caused him to imagine his guilt.

In his police confessions, Hernandez said that he had lured Etan into the basement of the bodega by offering him a soda, strangled him, packed the boy’s body into a produce box and lugged it to a trash bin two blocks away.

Hernandez did not give a motive, saying only that “something took over me,” but prosecutors believe he tried to sexually assault Etan.

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Both trials were hotly contested. Prosecutors had no body to even prove a murder occurred, and no forensic evidence, but they portrayed Hernandez as the missing piece in a jigsaw puzzle — a man at the right place at the right time who fit the known facts and left New York to seek forgiveness at a religious retreat within weeks of Etan’s disappearance.

The defense, however, portrayed Ramos as a far more likely suspect, a man with a string of molestation charges, unlike Hernandez, a father — his daughter testified on his behalf — whose record was clean except for the Patz allegations. The defense also called mental health experts, whose conclusions about Hernandez’s low IQ and mental disorder were contested by prosecution experts.

Jurors on Tuesday said their deliberations took a long time because of the amount of information they had to sort through from a three-month trial, but they were comfortable they got it right after 37 years.

“We worked a long time,” said juror Michael Castellon. “We came to a clear, logical result.”