The Road star, who dated the Irish actor for nine years after meeting on the set of the 2001 film Trapped, has allegedly told friends that she split from Townsend after a trip to Mexico over the Christmas holidays.
A source told The Mail On Sunday: "Stuart is gutted but Charlize said that she realised during the Mexican holiday the relationship was over. They had become more like brother and sister than lovers. It was she who ended it."
The 34-year-old actress is said to be living in the couple's main home in the Hollywood Hills, while Townsend has moved his belongings into their beach house.
The source added: "She loved Stuart but their relationship ran its course. He is heartbroken but she is insisting it is over. Charlize was surprised the story hadn't come out yet. But she didn't confirm it because she wanted to break the news in her own time."
When the newspaper asked for confirmation, Theron's spokesperson said: "I never comment on her personal life."
Theron recently revealed that she is ready to start a family.