Ambulance paramedics found Flynn unresponsive and doctors later diagnosed head and brain injuries and bleeding on the spinal cord and found bruises on his scalp and lower body. Flynn died four days later.
Staples, 35, was jailed for nine years on Thursday, to serve seven years before he is eligible for parole.
He pleaded guilty to child homicide, a charge similar to manslaughter that applies to young children, although Staples claimed for weeks that Flynn must have been injured in a fall from a change table onto the carpeted floor.
The Supreme Court heard that on the day after Flynn was injured, Staples told Ms Hall and police he heard a thud from the baby’s room and found Flynn on the floor.
The next day Ms Hall ended their relationship when she discovered Staples had left their son alone to buy alcohol and drank heavily that night.
Doctors knew Flynn’s injuries weren’t consistent with a fall from a change table but it wasn’t until about five weeks later that Staples told Ms Hall he was “too rough” with Flynn and put him down “pretty hard” as he changed his nappy and the baby went quiet.
Justice Paul Coghlan said Staples now accepted he caused his son’s injuries but couldn’t recall exactly what happened, although he denies shaking the baby.
“You will have to live with the death of Flynn and the consequence to the other victims for the rest of your life,” he told him.
Staples’ lies to Ms Hall and her parents aggravated his offending, the judge found.
“The effects of Flynn’s death and particularly the way it was caused have been devastating and life changing for them,” Justice Coghlan said.
“It’s true to say their lives will never be the same again.”
Staples was happy being a father but found it difficult, the court heard, and had been drinking heavily from before his son was born to help cope with the social anxiety he had experienced since his 20s.
He was later diagnosed with a personality disorder. Justice Coghlan said Staples’ personality traits made it difficult to express remorse but he understood the distress he had caused.
Staples, who used to work reading gas meters and restoring old cars, has already served 490 days.
For help in a crisis call 000. If you or anyone you know needs support, you can contact the National Sexual Assault, Domestic and Family Violence Counselling Service on 1800RESPECT (1800 737 732), Lifeline 131 114, or Beyond Blue 1300 224 636.
Adam Cooper joined The Age in 2011 after a decade with AAP. Email or tweet Adam with your news tips.