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The two sides announced a confidential settlement had been reached on Wednesday afternoon, after mediation ordered by the Federal Circuit Court.
"While it was not Rugby Australia's intention, Rugby Australia acknowledges and apologises for any hurt or harm caused to the Folaus," the organisations said in joint statement with Folau.
It's understood Folau is delighted with the settlement, and particularly the apology, which he had been seeking since the start of the dispute.
"Similarly, Mr Folau did not intend to hurt or harm the game of rugby and acknowledges and apologises for any hurt or harm caused," the statement said.
Folau had asked for $14 million in compensation for the sacking, while Rugby Australia said it was within its rights to sack him over his Instagram post in April which said "Drunks, Homosexuals, Adulterers, Liars, Fornicators, Thieves, Atheists, Idolators: Hell Awaits You. Repent! Only Jesus Saves."
"The social media post reflected Mr Folau's genuinely held religious beliefs, and Mr Folau did not intend to harm or offend any person when he uploaded the social media post," the statement said.
"Mr Folau wants all Australians to know that he does not condone discrimination of any kind against any person on the grounds of their sexuality and that he shares Rugby Australia's commitment to inclusiveness and diversity."
Rugby Australia and NSW Rugby said they "do not in any way" agree with the content of Folau's post.
"Inclusiveness is one of Rugby's core values and it welcomes all people to the game, including all members of the LGBTI community," the joint statement said.
"Rugby Australia and Mr Folau wish each other well for the future. The parties do not intend to comment further on the terms of their settlement as it is confidential."
Folau is a hardline Christian who belongs to the Truth of Jesus Christ Church in Sydney, after leaving his previous mainstream churches.
The former rugby league and AFL player recently attracted criticism after he said the deadly bushfires were God's judgement for same-sex marriage and abortion laws.