Denby Collins, 38, was tackled and restrained when he entered a house in Gillingham, Kent in December 2013.
His father challenged a law introduced in April 2013 giving householders the right to use "disproportionate force" against intruders.
The High Court has ruled the law is not incompatible with human rights laws.
Mr Collins was arrested as a suspected burglar by officers called to a house in Lower Rainham Road, Gillingham on 15 December 2013.
He was being restrained by at least one resident of the house when police arrived and was handcuffed at the scene.
Officers realised he was unresponsive and took him Medway Maritime Hospital from where he was transferred to the Royal Hospital for Neuro-disability in Putney.
He remains in a coma today.
The Independent Police Complaints Commission investigated the case but found there was no indication that any officer breached the standards of professional behaviour.
An officer believed to have handcuffed Mr Collins resigned from Kent Police in June 2014.
The so-called "householder defence" was introduced by a former Justice Secretary, Chris Grayling, to toughen up self defence laws "for those who defend themselves and their loved ones".
Mr Grayling wanted to demonstrate to the public that "the law is on their side".
Lawyers for Peter Collins argued that the law on self-defence in householder cases was incompatible with the European Convention on Human Rights.
Two High Court judges rejected the challenge but said the law did not "give householders carte blanche in the degree of force they use against intruders in self-defence".
Sir Brian Leveson said: "A jury must ultimately determine whether the householder's action was reasonable in the circumstances as he believed them to be.
The case arose after the Director of Public Prosecutions (DPP) decided in September 2014 not to prosecute the homeowner in the Collins case - referred to as "B" for legal reasons.
In a statement the family said they were disappointed with the court's ruling and were considering an appeal.
The father of a suspected burglar left in a coma after being tackled by a homeowner has failed in a legal challenge.