Azeem Rafiq had accused Vaughan of hurling racial abuses during his time with Yorkshire.
Rana, who was the club's overseas player at the time, was alongside Azeem Rafiq at Trent Bridge in 2009 when Vaughan is alleged to have said: "There's too many of you lot, we need to do something about it."
Rana and Azeem were among four players of Asian heritage in the Yorkshire team at the time.
Former England captain Michael Vaughan admitted that his name appeared in Yorkshire's report into Azeem's allegations of racism at the club. But in his column in the Telegraph, he rejected the suggestion he had ever said anything of the sort.
Michael Vaughan accused of racism by Azeem Rafiq; former England captain rubbishes allegations
But Rana confirmed to ESPNCricinfo that he heard Vaughan make the comments and has reiterated his preparedness to provide evidence to any inquiry as required.
Vaughan’s insinuation comes 24 hours after Gary Ballance admitted, via a statement issued by Yorkshire, that he had been the player who had used the racial slur "P**i" in conversations with Rafiq.
Roger Hutton, Yorkshire chairman, has since resigned from his post amid the fall-out at the club, which includes Headingley's suspension from hosting international and major matches, and the loss of a raft of sponsors, including Emerald, Nike, Tetley's, and Yorkshire Tea.
(ESPNCricinfo/ANI inputs)