Stephen Waterson, 26, reversed the seat of his Audi convertible, squashing three-year-old Alfie Lamb in the footwell behind on a journey home on February 1 last year.
Waterson, described by police as being "arrogant, selfish and deeply unpleasant", then lied to police about what happened and threatened his girlfriend and two friends who were also in the car.
Following a trial, Alfie's mother, Adrian Hoare, 24, from Gravesend in Kent, was jailed for two years and nine months for child cruelty.
Ahead of a retrial at the Old Bailey, Waterson admitted manslaughter by gross negligence.
Mr Justice Kerr sentenced Waterson to five years and six months for the manslaughter.
The judge said: "I do not find you were annoyed with Alfie and moved your seat back because of that annoyance."
But he said he was satisfied he moved his car seat back twice "for your own comfort".
He accepted character references from Waterson's parents, who attended court, and agreed he was "not all bad".
But he added he was "cunning, manipulative, threatening, and controlling".
He handed him a further two years for intimidation and 18 months for conspiracy to pervert the course of justice to run concurrently with each other and consecutively to the manslaughter sentence.
Both Waterson and Hoare had admitted conspiring to pervert the course of justice by lying to police.
Waterson was also convicted of intimidating witness Marcus Lamb and Hoare of assaulting another witness, Emilie Williams.
Pregnant barmaid Williams, 20, had admitted conspiring to pervert the course of justice after being threatened and "coerced" into lying to police by Waterson.
Williams, who is due to give birth in January, was sentenced to five months imprisonment suspended for 18 months and 100 hours of unpaid work, to be completed after she gives birth.
On the cover-up after Alfie's death, Mr Justice Kerr told Waterson: "You orchestrates a campaign of lies, assisted by Ms Hoare who had the misfortune to fall in love with you and was willing to lie to protect you and herself.
"You exploited the vulnerability of Ms Williams, who was frightened of you."
It is the first time anyone in the UK has died from crush asphyxiation as a result of an electronic car seat, police said.
In mitigation for Waterson, Tana Adkin QC told the court: "Whilst thoughtless, I have no doubt, and selfish in his behaviour on February 1, he was not deliberately malevolent and nasty towards Alfie."
Speaking outside court, Alfie's aunt Ashleigh Jeffery said: "No sentence will be enough but today we finally gave Alfie a voice and justice has been done."
She said the family was "utterly devastated" by Alfie's death.
Ms Jeffery said: "He was a very happy three-year-old boy with his whole life ahead of him."
She said the family would never come to terms with what happened and had been through a "very traumatic" police investigation and court trial.
She added: "We hope that we can move forward in private with our treasured memories of Alfie."
In a statement read in court, she added: "Every time I saw Alfie, he was so happy. He always wanted to play and had such a bright imagination. He had the best smile and he was always smiling.
"Alfie's death has had such a profound effect on me, my life, my health, my children, my relationship.
"When I found out that Stephen had pleaded guilty to the manslaughter of Alfie it was like a huge weight had been lifted but it also made it all feel so much more real. He could have avoided so much more upset in people's lives had he just owned up in the beginning."
The court heard that the defendants had gone shopping for cushions in Sutton, south London, accompanied by Alfie, Williams, Marcus Lamb, 22, and another young child.
Jurors in the earlier trial were shown CCTV of Alfie running to keep up with his mother moments before he was put in the car for the journey back to Croydon, south London.
The court had heard that nightclub worker Waterson became annoyed at Alfie's crying and moved his front passenger seat into him as he sat at his mother's feet.
The maximum space in the footwell was 11.8in (30cm), and, at the touch of a button, that could be reduced to just 3.7in (9.5cm).
When Alfie continued to moan, Waterson reversed again, saying: "I won't be told what to do by a three-year-old", Hoare told jurors.
By the time they arrived at Waterson's home in Croydon, the little boy had collapsed and stopped breathing.
As medics desperately tried to revive him, Waterson fled the scene and Hoare spun a web of lies to protect her boyfriend, claiming she had been in a taxi.
Alfie, nicknamed "Little Tarzan" by the defendants, died from crush asphyxia three days later.
As police closed in, Waterson gave officers a false name and false statement, and sold the Audi.
He threatened to make Hoare and the other witnesses "disappear" if they did not stick to their fake stories.
Hoare eventually broke her silence and told her half-sister, Ashleigh Jeffrey, what happened in a taped conversation handed to police.
But Waterson blamed Mr Lamb, whom he regarded as a stepbrother, for being a "grass" and put his foot on his head during a violent assault in Crystal Palace Park, which was filmed on his mobile phone.
Jurors in the first trial were told that Waterson was a controlling womaniser who also had a violent temper, with three previous convictions for attacking an ex-girlfriend and his sister's husband.
Giving evidence earlier this year, he denied he would hurt a child and said he moved his seat back once by up to an inch.
Waterson's father was first elected MP for Eastbourne in 1992 and was a junior minister in John Major's government, but was defeated by Liberal Democrat Stephen Lloyd at the 2010 general election.