The Dublin native was not at the side of South African actress either at last week's Oscar ceremony in Los Angeles or the Bafta ceremony in London the week before, The Sun noted Saturday.
The Sun quotes a friend of Theron's saying: "Charlize is free and single again. Her relationship with Stuart is well and truly over."
The friend said the duo "just grew apart."
Theron, 30, was quoted a few weeks ago as saying she would never marry the 33-year-old star of "The League Of Extraordinary Gentlemen."
"It's not really what I want -- or what he wants," the Sun quoted her as saying.
2014: The Year in Fashion [PHOTOS]
Say bye bye to Honey Boo Boo