Kyle Campbell, 27, killed little Riley Siswick "either from a fist or by jumping or stamping on him or by striking him with an object" in February 2016.
Riley was found dead two days after he was seriously injured by Campbell at their Huddersfield home, Leeds Crown Court heard.
Campbell's actions "condemned Riley to a slow and painful death and deprived him of any residual chance he had of survival", the court was told.
He was found guilty of murder by a jury following a six-week trial.
Campbell was jailed for life with a minimum term of 20 years.
Riley's mother, Kayleigh Siswick, 27, was also found guilty of causing or allowing the death of a child.
She was today (Thurs) jailed for seven years.
Both showed no emotion as they were sentenced.
The judge, Mr Justice Turner, said that by not seeking medical help for Riley after Campbell attacked him in February 2016, the pair condemned the boy to 36 hours of "unremitting and significant pain".
The judge said Campbell's decision to go along with other people's concerns that Riley had a severe stomach bug was a "reckless gamble" that "did not pay off".
He told him: "You were too much of a coward to face up to the consequences of your actions and pretended that nothing had happened."
Instead, the judge said: "He (Riley) was left to die in a bed soaked in his own urine".
The judge said he was satisfied that Siswick "prioritised" her relationship with Campbell over her children.
However, he said he had reduced her sentence to reflect that, with "limited cognitive abilities" and a mental age of 11, she had a "lack of insight" into her actions.
The judge told her this "considerably diminished your responsibility".
Detective Chief Superintendent Nick Wallen, who led the investigation for West Yorkshire Police, said: "This has been a very long and complicated investigation. Riley, who was just three years old, suffered a catastrophic injury and details of how this could have been sustained were heard throughout the trial and subject of expert medical evidence.
"We are really pleased we have been able to secure justice for Riley."