For almost a quarter of a century, a coterie of the nation’s most elite universities had a legal shield: They would be exempt from federal antitrust laws when they shared formulas to measure prospective students’ financial needs.

But the provision included a crucial requirement: that the cooperating universities’ admissions processes be “need-blind,” meaning they could not factor in whether a prospective student was wealthy enough to pay.

But a court filing on Tuesday night revealed that five of those universities — Brown, Columbia, Duke, Emory and Yale — have collectively agreed to pay $104.5 million to settle a lawsuit accusing them of, in fact, weighing financial ability when they deliberated over the fates of some applicants.

Although the universities did not admit wrongdoing and resisted accusations that their approach had hurt students, the settlements nevertheless call into question whether the schools, which spent years extolling the generosity of their financial aid, did as much as they could to lower tuition.

Brown University maintained that all financial aid decisions were made in the “best interests of families and within the law,” but in a statement on Tuesday night, said resolving the case will permit it to “focus its resources on further growth in generous aid for students.”

The agreements from the five universities came months after the University of Chicago agreed to pay $13.5 million to settle its portion of the case. Other schools, including Cornell, Georgetown, Johns Hopkins, M.I.T. and the University of Pennsylvania, remain mired in the litigation, with no trial date set.