And Sean was great with all of that." Theron, 40, said when she expressed interest in wanting to adopt at least one more child, she'd hoped her relationship with Penn, 55, would "go somewhere" before that happened.
That next-level relationship, she said, "ultimately did not happen," and they parted ways, reportedly after vacationing together last May.
"We were very, very new in a relationship," she told the magazine, which published its Theron feature online Monday. So there was an understanding that I was a single mom with a very young boy who I had to put in a situation where he understood that Mommy dates but that he does not have a father, you know what I mean?
"The stories saying that Sean was going to adopt Jackson and all of that were not true. You have to be very careful and very honest about that stuff.
Lee was a former drug dealer by trade, convicted of espionage for the Soviet Union and originally sentenced to life in prison, but was paroled in 1998.
Penn later hired Lee as his personal assistant, partly because he wanted to reward Lee for allowing him to play Lee in the film; Penn was also a firm believer in rehabilitation and thought Lee should be successfully reintegrated into society, since he was a free man again.
Penn made his feature film directorial debut with The Indian Runner (1991), followed by the drama film The Crossing Guard (1995) and the mystery film The Pledge (2001).
Penn directed one of the 11 segments of 11'09"01 September 11 (2002), a compilation film made in response to the September 11 attacks.
In November 2008, Penn earned positive reviews for his portrayal of real-life gay-rights icon and politician Harvey Milk in the biopic Milk (2008), and was nominated for best actor for the 2008 Independent Spirit Awards.
The film also earned Penn his fifth nomination and second win for the Academy Award for Best Actor. Wilson in Fair Game (2010), a film adaptation of Valerie Plame's 2007 memoir.
His fourth feature film, the biographical drama survival movie Into the Wild (2007), garnered critical acclaim and two Academy Award nominations.