Pacino and D'Angelo did not disclose details of Monday's settlement, but both answered "Yes, your honor" when Manhattan Family Court Magistrate David Kirshblum asked if they agreed to the resolution of their own accord, E! Online reported.
As D'Angelo exited the courtroom, she said putting the matter to rest "feels terrific. I'm very happy," E! said.
The twins were born in 2001, four years after the couple began dating. Soon after the birth of their son and daughter, D'Angelo's first children, the couple reportedly began having problems.
Last year, Pacino sued D'Angelo for additional custody of the twins. The dispute was resolved, but no details were reported.
Pacino has an older daughter from a previous marriage.