Model Michael Girgenti requested the test from the 33-year-old reality star, after they allegedly slept together in 2009 when she was on a break from long-term partner Scott.
Lab results taken from tests run on August 12 have now proven the allegations wrong.
Kourtney, who has always denied the allegations, confirmed the news to an American channel.
'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,’ she revealed.
'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.'
However Girgenti is not ready to let the case rest, and his spokesperson has released a statement confirming he will be pursuing his claims.
‘We don’t trust the results and believe it could have been fixed. [We are] still going to court to fight for court ordered results.'
The lawsuit reportedly follows a warning letter the 26-year-old sent the star, who also has 13-month-old daughter Penelope with Scott, which reads:
‘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.'