The couple were recently the subject of tabloid reports that they were spending time together near Gyllenhaal's West Village apartment in New York City, having been set up by Holmes's Dawson's Creek co-star Joshua Jackson.
"Josh has been the mastermind behind this romance," a supposed friend of the pair has claimed.
Holmes's official spokesperson has since been reached for comment about the tabloid reports by Gossip Cop.
"[It's] not at all true [that Holmes and Gyllenhaal] are secretly dating," the representative insisted.
The tabloid reports linking Holmes with Gyllenhaal came at the same time as rumours of a romance between her ex-husband Tom Cruise and Cynthia Jorge were also downplayed.
Cruise and Holmes reached a divorce settlement in August after five years of marriage.