The celebrity couple, who have a son together, Henry Chance, are seeking joint custody of their four-year-old.
A joint statement issued on behalf of the Hollywood actress and Aronofsky, who were engaged but did not marry, said that they had split up some time ago and did not give a reason for the break-up.
It said: "Rachel Weisz and Darren Aronofsky have been separated for some months.
"They remain close friends and are committed to raising their son together."
Weisz's credits include The Mummy, The Lovely Bones and My Blueberry Nights.
She won a best supporting actress Oscar for The Constant Gardener in 2006.
Earlier this year, she worked on upcoming film The Dream House with James Bond star Daniel Craig.
US director Aronofsky, 41, enjoyed acclaim with The Wrestler, starring Mickey Rourke, and his next film, Black Swan, starring Natalie Portman, has been tipped for Oscar glory.
Cambridge graduate Weisz, who was born in London, the daughter of Hungarian parents who fled Nazi Germany to settle in Hampstead