The actress - who has been working in Hollywod for more than 14 years - said she ran out of the room.
Scott said she later came across Pardue while about to leave the set of Mogulettes and asked him why he masturbated in front of her. The actress claimed that Pardue - whose credits include Remember The Titans and Thirteen - told her because she was "just so hot".
Pardue when contacted by The Times apologized for putting Scott's hand on his penis while on set, but denied her other allegations.
"I clearly misread the situation during a sex scene on set and have apologized to Sarah," Pardue said in a statement from his representative David Shane. "I never intended to offend her in any way and deeply regret my actions and have learned from my behavior."
Scott recounted her odyssey reporting the alleged misconduct with the SAG-AFTRA union and the Time's Up Legal Defense Fund in the wake of the Harvey Weinstein sexual misconduct scandal and the #MeToo Movement.
The actor's guild scheduled a disciplinary committee hearing for October 26, but it was postponed after both parties jointly agreed to enter mediation, the DailyMail reports.
If either side is dissatisfied with the mediation outcome, a guild hearing can still proceed.
The guild's disciplinary committee could decide if Pardue should be expelled or suspended, which could mean the loss of work and possibly health insurance.
"I am disappointed that Kip has chosen to hide behind his actions," said Scott, who also filed a report with the Hermosa Beach Police Department in August to put the matter on record.
"Speaking out about this has been extraordinarily difficult for me, and now I understand why so many people don't. My goal remains the same — my wish is for Kip to take full responsibility for all of his actions," she added.
The 15-year union member also said that despite nearly six months of pursuing her case, she remained hopeful that Hollywood will change.
"I was sexually violated while at work, and even though I had the courage to tell anyone and everyone who'd listen, as time went on it seemed like I had very little control in truly preventing this from happening to anyone else," she said.
Pardue is a main cast member of Marvel's Runaways on Hulu and plays Frank Dean.