Wells was never charged after an Ohio prosecutor said there was no basis for charges, The Baltimore Sun reported Tuesday.
The suit, which names the university and president the Rev. Michael J. Graham as defendants, claims Xavier failed to follow established school disciplinary policies in expelling him.
The university's conduct board "conducted a fundamentally unfair hearing and defamed Wells by publicly proclaiming him guilty of rape, materially as a result of Father Graham's irresponsible and reckless rush to judgment," the suit alleges.
In an e-mailed statement, Xavier defended its procedures, saying, the suit's claims were "unfounded and cannot be supported."
The university said the procedures that resulted in Wells' expulsion are "the standard used in all American universities."
Xavier added, "The university has never revealed the specific charge against Dez Wells other than to say he was found responsible for a violation of the Student Code of Conduct."
Wells transferred to the University of Maryland before last season and immediately became a starter.
Hamilton County Prosecuting Attorney Joseph T. Deters, who declined to file charges against Wells, has said Wells had been involved in a game of "truth or dare" involving three females and three males that led up to the accusation. The accuser's "dare" had been to hold up her shirt, and she did so. She and Wells later had sex, which Deters described as "totally consensual until the very last seconds, and that's where their stories diverged,"