The Oscar-winning actor, 46, was found dead in his Manhattan apartment earlier this month from a suspected heroin overdose.
As mother to the couple's three children – Cooper, Tallulah, and Willa – Mimi was named executor of Philip's estate. While the exact value of the property is unknown, the papers filed set it at more than £300,000.
Philip drew up the will in October 2004 and made specific stipulations for his eldest child, ten-year-old Cooper.
At the time, Philip had separated from Mimi, who is described in the will as his "friend and companion," reportedly because of heroin abuse.
The late star, who won his Best Actor Oscar for Capote, arranged for a trust fund to be set up for Cooper. Philip also expressed a "strong desire" for his son to be raised in New York, Chicago, or San Francisco – and if not, to visit at least twice a year to experience their "culture, arts and architecture".
"The purpose of this request is so that my son will be exposed to the culture, arts and architecture that such cities offer," the will read.
As Philip's other children had not been born yet, there was no specific mention of Tallulah, seven, and Willa, five. The accompanying papers to the will however noted Philip's daughters and the situation.
Mimi and her children live in Manhattan's West Village, not far from Philip's Greenwich Village flat where he was discovered on 2 February.
The cause of Philip's death is still being investigated as medical examiners are awaiting further tests. The will filings say simply that he "died suddenly".
A week after Philip passed away, his family and a host of celebrities who were close friends with the Hollywood star and had worked with him gathered to attend his wake.
A private funeral service for relatives and close friends was also held, while a larger memorial service is expected to take place later this month.