The former couple were in a secret relationship, about which Madonna has only recently spoken publicly.
The singer and Ms Lutz fell out in 2003, and after settling a legal dispute over artwork the following year, Madonna signed a release from "any and all" future claims against her former friend, Judge Gerald Lebovits said in his ruling made public on Monday.
As such, he explained, the pop star could no longer sue over the items subject to auction.
Madonna told the court last year when she sought an injunction on the sale that her celebrity status "does not obviate my right to maintain my privacy, including with regard to highly personal items".
Ms Lutz's lawyers have accused Madonna of a "personal vendetta".