The couple - who have a four-year-old son, Henry Chance, together -called time on their nine-year relationship several months ago, their representatives have confirmed.
A spokesperson told gossip website TMZ: "RachelWeisz and DarrenAronofsky have been separated for some months. They remain close friends and are committed to raising their son together in New York City."
It is believed the couple will seek joint custody of their son.
No reasons for their split have been given.
Rachel and director Darren, 41, previously worked together on 2006`s `The Fountain` and were also planning to team up for `Jackie`, a biopic of former American First Lady Jackie Kennedy.
The 40-year-old actress has previously spoken about how much she enjoyed leading a "normal" life with her partner and son.
She said: "Of course, it`s not ordinary to get dressed in frocks to walk down red carpets and travel all over the world and stay in five-star hotels.
"I`m not working in a factory. But I drop Henry off at school, I pick him up. I try my hardest to keep everyone together.
"I am interested in playing extra-ordinary women, but I have an ordinary life."
Rachel has also spoken about how she and director Darren juggle their work commitments in order to provide a stable environment for Henry.
She explained: "I have to consider where I`m travelling to if Darren`s going to be working at the same time.
"I filmed `Agora` in Malta for four months and Darren edited there. I started and he came out two weeks later with his editor. Before that we were both at home in New York, so we`ve managed to keep the family together and it works."