Michael Girgenti, a male model filed a paternity suit last week, in which he claimed that Mason was his son and a result of their affair in 2009, reported TMZ online.
Girgenti alleged that when he saw photographs of Mason he saw a striking resemblance and knew he was the father. He attempted to file for joint custody of Mason and requested DNA tests.
A hearing was set for next month although the claims, owing to the new evidence, may now be dismissed.
"After three-and-a-half years of rumours and 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," Kourtney said.
"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," the 34-year-old added.
The 'Keeping Up With The Kardashians' star has been dating Disick since 2006 and the couple have two children together- three-year-old Mason and one-year-old Penelope.