The 40-year-old actress denied she suddenly and completely cut off communication with the 55-year-old actor in a new interview with the Wall Street Journal.
"There is this need to sensationalize things," Theron explained. "When you leave a relationship there has to be some [expletive] crazy story or some crazy drama. And the [expletive] ghosting thing, like literally I still don't even know what it is."
"We were in a relationship and then it didn't work anymore," she asserted. "And then we both decided to separate. That's it."
Theron and Penn dated for over a year before splitting in summer 2015. The couple seemed to be heading toward marriage and having Penn adopt Theron's son Jackson, but in reality, the relationship never reached that level of commitment.
"The stories saying that Sean was going to adopt Jackson and all of that were not true," the actress revealed. "It's not something that happens in 18 months ... You have to be very careful and very honest about that stuff. And Sean was great with all of that."
"[I was honest] about wanting to have more kids, [but] there was an understanding that a relationship had to go somewhere before it was going to be -- what you hope for, which ultimately did not happen," she explained.
Theron adopted her second child, daughter August, shortly after her split from Penn. The actress previously expressed her desire for a family in the May 2012 issue of British Vogue shortly after announcing Jackson's adoption.
"I've always been very honest in saying I wanted a family. I've always known I wanted a family," she said. "[I hope] to be like my mom. Fair, tough, loving and supportive. My mom has made it possible for me to be who I am. Our family is everything."