Allan Young, 36, broke down in tears at the Old Bailey as the jury returned a verdict of not guilty in the landmark case after his son died more than a decade after he was injured.
Mr Young had previously been jailed for 12 months after admitting causing grievous bodily harm to five-week-old Michael Winn in 1998, leaving him "severely disabled", the court heard.
When Michael died in 2011, Mr Young was further 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 date of the original assault.
In Mr Young's case, charges were brought even though there had been a 12-year gap, making it the longest on record.
The prosecution said Michael's death was a direct result of the injuries he suffered years earlier which caused cerebral palsy and curvature of the spine.
His physical and intellectual development was impaired to such an extent he had trouble breathing, was blind, incontinent and could not speak.
Following the assault, Michael was assessed as having only a 65% chance of surviving to the age of 11, the court heard.
Mr Young, of Wishaw, North Lanarkshire, had denied manslaughter. He declined to comment as he left the court.
Mr Young was unemployed and living with his partner Erica Francis in London, when he shook his baby in 1998, the court heard.
At the Royal Free Hospital in London, a CT scan revealed he had suffered bleeding on his brain and he was diagnosed with "shaken baby syndrome".
Both parents were arrested and Mr Young was charged with inflicting grievous bodily harm.
On January, 2011, Michael's adoptive mother Karen Heppleston-Winn saw Michael's breathing had stopped and he died overnight on January 23 2011, at the age of 12.
Mr Young was arrested in March 2011 and told police in an interview that he had "accidentally shaken" Michael for mere seconds after he had been up all night, the court heard.
At the conclusion of the trial, Mr Young simply bowed his head before breaking into tears as the jury foreman returned the not guilty verdict.
He later sobbed as he hugged a supporter.