Michael Girgenti had alleged that he was Mason's father and brought a paternity lawsuit against Kourtney, claiming that he had had a short-lived romance with the reality star around the time she fell pregnant.
But lab results from tests taken on 12 August have proved he is not Mason's father.
Kourtney, who has always denied Michael's claims, told E! News, "After three-and-a-half years of lies being spread by an individual I met briefly at a photo shoot, I am setting the record straight that Scott is Mason's father.
"While it saddens me to have to address these ridiculous lies — especially when the truth was never in doubt — this story must be put to rest."
Despite that, Michael, 26, appears not to have accepted the findings.
"We don't trust the results and believe it could have been fixed," his spokesperson told Radar. "Still going to court to fight for court-ordered results."
Before taking the case to court, Michael reportedly wrote a letter to Kourtney urging her to submit to a DNA test.
According to Radar Online, the letter, dated 23 April, said, "My attentions (sic) are not to hurt the family you've created with Scott.
"Please take this final request for a DNA test seriously. Because if you don't, I will be forced to take legal action and sue.
"I assure you I don't take being a father lightly. I will be a great father to Mason."
Kourtney was said to be "furious" over his claims. Her attorney Todd Wilson had previously described Michael's allegations as "absurd".
"This individual has been selling false and fabricated stories to the tabloids for years about Kourtney Kardashian and her son, Mason," Todd Wilson told E! News. "Scott Disick is Mason's father.
"We have not seen the reported court filing, but we are informed that this individual has been seeking to get paid to publish his ridiculous pleading.
"His claims are absurd and this is simply another shameful attempt to gain publicity and profit from fictional stories about my client."
Kourtney and Scott, 30, started dating in 2006. Mason was born in December 2009, followed by their daughter Penelope in July 2012.