The pair sparked speculation their romance was in trouble when the actress failed to attend the Cannes film festival in France last month with Sean for his film 'Tree of Life.'
Instead, she was said to be concentrating on her new film 'The Avengers' in New Mexico, where she is reprising her role of Black Widow from 'Iron Man 2.'
Now a source has confirmed to People magazine they have split, although the reasons behind their parting are not yet known.
Scarlett, 26, and Sean, 50, started dating in February, shortly after the ‘Lost in Translation’ star split from husband Ryan Reynolds, and in April sources suggested they were already moving in together.
An insider said the actress had "essentially moved in over the last few weeks," to the ‘Milk’ actor’s $3.8 million Malibu home.
Scarlett initially struck up a friendship with Sean – who divorced wife Robin Wright in 2010 after 13 years together - when she was considering flying to Haiti to help people affected by the two earthquakes in January 2010.
A source explained: "Scarlett first reached out to Sean when she was planning to visit Haiti with Oxfam. She knew Sean was living there in a tent and turned to him for advice."
Although Scarlett wasn't able to make the trip, the couple started dating and made their first public appearance together at the wedding of Reese Witherspoon and Jim Toth in March.
They were then spotted at a number of public engagements together, including a White House Correspondents' Dinner party in Washington D.C. in April.
Representatives for the couple declined to comment.