Fischer, 66, said in a brief statement that he “now regretted the resulting situation for which I am responsible” and decided to step down immediately, instead of in July 2014 as previously intended.
His decision to fire associate professor Iris Ritzmann was contested, with 500 professors and scholars signing a petition in her support, saying she was a “scapegoat” in the affair, the SDA news agency reported.
And the university, in a separate announcement on Wednesday, said it was reconsidering her case.
The leaked information concerned Mörgeli, who was fired in September 2012 as the director of the university's Medical History Museum following a performance review.
The university maintained that he had mismanaged the museum and acted disloyally by publicly criticizing his superior but his post as professor was not affected.
But the university filed a complaint with the canton of Zurich’s public prosecutor’s office after Mörgeli, who is also an Swiss People’s Party federal MP, released confidential information at an April press conference in which he contested the way he had been treated.
Ritzmann, meanwhile, was fired after she sent to the Tages Anzeiger newspaper an internal document that gave a poor review of Mörgeli’s performance, the SDA news agency reported.
The university maintained that once that confidential information became public it was compromised in its evaluation of Mörgeli’s work.
Deputy rector Otfried Jarren will replace Fischer on an interim basis until a full-time appointment is made, the university indicated in a statement on its website.
Jarren told SDA that Fischer resigned out of “concern for the reputation of the university”.
In his statement Fischer said that in the seven and half years in which he served as vice-rector and then rector “much has been achieved”.
He added, “I am convinced that the university is well positioned for the future”.
Educated at the University of Basel and the University of Durham, in England, Fischer is among other things an editor of the journal Swiss Studies in English and a member of the board of trustees of the Zurich James Joyce Foundation.