Penn, 53, reportedly told Piers Morgan that Theron was "a keeper," and the two have been photographed together at multiple events. But the 38-year-old actress spoke publicly about her relationship for the first time with the magazine.
"Look, we're dating, and I don't think we were trying to hide anything," she said. "What I will say is, I was single for a really long time. I was enjoying mommy-hood. You just naturally become kind of selfish about your time, and all of it is dedicated to this little thing, whether he needs it or not."
Theron said she was unwilling to be in a relationship with a man unless he could add something to her life.
"What I guess I am trying to say is: A friend kind of stepped into that role, and I really didn't see it coming," she continued. "Sean and I have known each other for eighteen years. We were just really good friends. And it's been slow going because you are aware that you could screw that up and lose it. We had to think about it."
"But at the end of the day, it was somewhat effortless," Theron said. "It just kind of naturally happened, and before I knew it, I was in something that was making my life better -- the people who really love me can see the effect it has had on me."
"And watching other people getting married? I think it's beautiful for them, but to be quite honest, usually I'm sitting there just devastated," she said. "It's supposed to be this night of celebrating love, and all you see is a couple separated all night making sure everybody else is OK. It just looks like a lot of work. And as you get older, you start sifting through the stuff that really matters."
The June issue of Vogue hits newsstands May 27, while her latest film, A Million Ways to Die in the West, premieres May 30.
Notable deaths of 2014 [PHOTOS]