Pregnant Jones recently announced she is expecting her first child later this year, just months after splitting from comedian Jason Sudeikis, but she has so far refused to name the child's dad.
Vaughn, the husband of supermodel Claudia Schiffer, found himself at the center of speculation this week when sources told E! News the director had developed a "very close relationship" with Jones while shooting their new action movie X-Men: First Class.
The claims were further fueled by the filmmaker's noticeable absence from the New York premiere on Wednesday.
But Vaughn's lawyer Martin Singer has blasted the rumor, branding it an "absolute lie."