McGregor, 36, shook his head as the jury returned their verdict awarding damages of 248,603 euros ($258,559) to Nikita Hand, who brought the case at Dublin's High Court.
The court was told that McGregor allegedly "brutally raped and battered" Hand in December 2018 but the Irish sports star claimed they had consensual sex.
Speaking after the verdicts Hand, 35, told reporters: "I hope my story is a reminder that no matter how afraid you might be: Speak up, you have a voice and keep on fighting for justice."
She thanked her family including her daughter, Freya.
"She has given me so much strength and courage over the last six years throughout this nightmare to keep on pushing forward for justice," she added.
"I want to show Freya and every other girl and boy that you can stand up for yourself if something happens to you –- no matter who the person is –- and justice will be served."
The standard of proof is lower in a civil case than a criminal one with the jury asked to decide the case on the balance of probabilities rather than beyond reasonable doubt.
Although the jury found in Hand's favour in connection with her accusation against McGregor, she lost an assault lawsuit against a second man.
The court heard evidence over two weeks from witnesses, including Hand, who has no automatic right to anonymity in the case.
Hand added that she had been "overwhelmed and touched by the support" she had received.
"For every person who reached out to me -– a card, a letter, an email, everything –- it hasn't gone unnoticed. Thank you, I really appreciate it so much," she said.
Appeal
Irish national broadcaster RTE reported earlier this month that Hand had been "absolutely devastated and let down" after the Director of Public Prosecutions told her that they would not be prosecuting either McGregor or the second man over her allegations.
She sought a review of the DPP's decision, but it was upheld.
Hand suggested that the DPP was not prosecuting because one of the suspects was a famous person, RTE reported.
McGregor is one of the biggest stars in the history of the Ultimate Fighting Championship (UFC) mixed martial arts circuit, formerly holding the featherweight and lightweight titles.
The DPP's office, however, said the director herself had reviewed the file personally but that the case was very complex and there was no reasonable prospect of a conviction for either man.
In a statement on X, McGregor said he intended to appeal.
"I am disappointed that the jury did not hear all the evidence that the DPP reviewed. I am with my family now, focused on my future," he said.
"Thank you to all my support worldwide," he added.
McGregor made headlines in November last year when he sent a series of social media posts during unrest in Ireland, criticising the government's immigration policy.
