A man who spent nearly 30 years behind bars for shaking his girlfriend’s baby to death has been freed after new evidence suggested the infant may have died from pneumonia.

Stephen Martinez had admitted shaking 4-month-old Heather Mares and banging her head against her crib in his Denver home in 1998, and was sentenced to life without parole two years later for first-degree murder.

However, his attorneys successfully argued that the fatal injuries most likely came from complications from pneumonia, with bleeding and swelling of the brain mistaken for so-called “shaken baby syndrome.”

Martinez’s conviction was vacated Tuesday after prosecutors admitted they could no longer prove beyond a reasonable doubt that he had killed baby Heather — whose mom, Kim Estrada, burst into tears in the courtroom, because she still maintains her ex is guilty.

Martinez — who had a leg amputated while in prison — was met by cheering supporters as he left the Department of Corrections Denver Reception and Diagnostic Center in a wheelchair. He was also met by his wife, whom he married behind bars.

“I’m so happy and so thankful to be out after being locked up for 27 years, innocent,” Martinez said, according to CBS News. 

“But now I’m going out to absolutely nothing. But God bless you, guys, have a great day.”

Martinez had called 911 to his Denver home in 1998, telling emergency workers that Heather was choking.

Responders found the baby was suffering a brain injury, with bloody sheets thrown in the laundry, according to court documents obtained by 9 News.

Martinez admitted shaking the crying girl and hitting her head against a crib — but insisted that he did not intend to hurt her.

Instead, they now maintain the dead injuries were from pneumonia. “Everything that you see, all of those injuries, stems from that,” one of his attorneys, Jeanne Segil, said in court, according to CBS.

However, the baby’s mom, Kim Estrada, and dad, Chris Mares, still blame Martinez for their child’s death, raging at him for showing no remorse.

“My life was stopped 27 years ago,” the heartbroken mom said outside the courthouse.

Hetaher’s uncle, Andre Mares, also said that the decision “doesn’t make sense.”

“How does a pneumonia cause a fracture on a baby’s head? How does Stephen admitting that he hit Heather’s head on the crib, how does pneumonia take all that stuff away?” he asked.

District Court Judge Andrew Luxen apologized to the parents as he dismissed the conviction and ordered Martinez’s release from prison.

“The loss that you and your family have suffered is incomprehensible. Especially for such a small child. I understand that today is a difficult day,” the judge told them, according to CBS News.

“I want you to know that this is not an easy decision. And I feel for you and your family.”

The case was brought to the Denver District Attorney John Walsh’s office by the Korey Wise Innocence project, which provides free investigative and legal services to people wrongfully convicted of crimes in Colorado.

The organization “presented my office with multiple credible medical experts who challenged the initial determination that Heather’s death was caused by physical abuse,” Walsh said in a statement.

The state was “unable now to meet our ethical and legal burden of proof beyond a reasonable doubt, we were obliged to dismiss the case,” he said — but stressed there was “no misconduct” on the part of those who worked the initial investigation.

“This is simply an example of the criminal justice system being willing and able to reassess a case when necessary,” Walsh wrote. 

Martinez’s attorney, Segil — the innocence project’s assistant director — called the case “a tragedy on every front.”

“He lost over 27 years of his life in prison for a crime he did not commit,” Segil said.

“This was a tragedy; it was not a crime. Steven Martinez did not cause the baby’s death. Our hearts go out to the family of the baby. We just cannot imagine what they’re going through, and I know today was re-traumatizing for them, so they’re in our thoughts.”

With Post Wires