Thomas's ex-boyfriend was suing him in the High Court of England and Wales for allegedly hiding his HIV status and "failing to take reasonable care" to avoid giving him the infection.
Thomas wrote on Twitter he was "delighted to say that the legal case against me has been settled", adding that he paid his accuser £75,000 plus costs, calling this a "hugely positive outcome" for "my own mental health and that of my family".
He stressed he had not admitted guilt, saying: "I maintain my innocence in all the meritless allegations".
Lawyers for Thomas's former partner Ian Baum confirmed he had accepted a financial settlement, calling this a "significant vindication for our client after an eight-year-ordeal".
The law firm McCue Jury & Partners said this was possibly the first such civil court case where the claimant has recovered damages.
The pair were in a relationship between 2013-2016, with Baum saying he was HIV negative when he first became involved with Thomas, who since retiring from rugby has become a broadcaster and campaigner for lesbian, gay, bisexual, transgender and queer (LGBTQ) rights.
Baum, in court papers, said he noticed Thomas was taking pills from unmarked bottles only to be told they were multi-vitamins.
But he said he found out ex-British and Irish Lions skipper Thomas had HIV after discovering a tablet marked GSK1.
"On googling the GSK1 pill, the claimant discovered that the defendant was taking anti-viral HIV medication," documents said.
"By transmitting HIV to the claimant, the defendant has caused him serious physical and psychological injury," the papers said.
Baum alleges Thomas used "coercive and controlling behaviour" to prevent his HIV status becoming public knowledge.
Thomas made sporting history by becoming the world's first openly gay rugby union player in 2009.
His playing career saw Thomas win a 100 caps for Wales, appear in four Rugby World Cups and also captain the Lions in 2005.
Thomas publicly revealed he was living with HIV, which if not treated can lead to the potentially life-threatening AIDS (acquired immunodeficiency syndrome) in 2019.
He is a patron of the Terrence Higgins Trust, an HIV and sexual health charity.
