A tearful Allan Young, 36, questioned whether the public interest was served by attempting to convict him for the manslaughter of Michael Winn.
Mr Young, of Glasgow Road in Wishaw, broke down in tears at the Old Bailey as the jury returned a verdict of not guilty following more than 24 hours' deliberation.
Mr Young was previously jailed for 12 months after admitting causing grievous bodily harm to five-week-old Michael in 1998, leaving him "severely disabled" with catastrophic brain injuries said to have led to the child's death in 2011, the court heard.
When Michael died, Mr Young was charged with manslaughter following a change in the law.
Before 1996, charges of murder or manslaughter could only be brought if death occurred within a year and a day from the assault. In Mr Young's case, charges were brought after a 12-year gap, making it the longest on record.
Speaking outside the court, through his solicitor Jenny Wiltshire, he said: "There are no winners in this case, or in relation to what happened to Michael. I had moved on with my life, with my new partner and lovely little girl.
"I really question whether it was in the public interest to prosecute me after so long." He added: "The effect has been devastating for me and my family. But I thank the jury for the care they gave to this difficult and sensitive case. I know there are others who share my grief for the illness Michael suffered and his death. I hope they like me can now move on."
The prosecution said Michael's death was a direct result of the injuries he had suffered years earlier, which caused cerebral palsy and curvature of the spine.
His development was impaired to the extent that he had trouble breathing, was blind, incontinent and could not speak.
Mr Young denied manslaughter and yesterday, after 24 hours and 40 minutes' deliberation, a jury of 10 people found him not guilty.
The court heard Mr Young was unemployed and living with his partner Erica Francis in London in 1998 when he shook his baby.
Miss Francis then noticed Michael had become "all floppy" and had "staring eyes that did not focus". At first, she thought Michael had flu, but the next day he was still the same, prosecutor Zoe Johnson QC said. She decided to call the health visitor, prompting Mr Young to admit he "may have hurt Michael" and shaken him because he would not stop crying, the court heard.
When the baby arrived at the Royal Free Hospital in London, he was "pale and fitting".
A CT scan revealed he had suffered bleeding on his brain and he was diagnosed with "shaken baby syndrome".
He was taken into the care of Camden social services and adopted while both parents were arrested and Mr Young was charged with GBH.
On January 11, 2011, his adoptive mother saw Michael's breathing had stopped and despite the efforts of medics, he died overnight on January 23, 2011 at the age of 12.
A post-mortem examination found he died of "respiratory insufficiency caused by pneumonia and the marked curvature of the spine" as a result of the injuries Michael had suffered as a very young infant, Ms Johnson said.
Mr Young was arrested in Scotland in March 2011 and told police he had "accidentally shaken" Michael for seconds after he had been up all night, the court heard.
At the conclusion of the trial, Mr Young bowed his head as the jury foreman returned a not guilty verdict, before breaking into tears.