Theron, who played the evil queen opposite Stewart's Snow White, is a good friend of Sanders' wife Liberty Ross.
The actress apparently feels betrayed by Stewart as she had become quite close with her during the shooting of the movie, reported People magazine.
"Charlize is absolutely fuming with Kristen for having an affair with Rupert. She is very tight with Liberty, has often socialized with the family over dinner, and cannot believe Kristin has done this," a source said.
Stewart, 22, issued a public apology this week after her affair became public. Sanders, who has two children with Ross, followed suit.
The 'Twilight' actress is reportedly struggling to save her relationship with Robert Pattinson.
"This momentary indiscretion has jeopardized the most important thing in my life, the person I love and respect the most, Rob. I love him, I love him, I'm so sorry," Stewart had said in her statement.