Annette Schavan stepped down from government after the University of Düsseldorf found she had systematically quoted the work of others without proper reference in her PhD thesis, published in 1980.
However, Ms Schavan, who became federal science minister in 2005 and led the multi-billion euro university investment programme, known as the Excellence Initiative, told a press conference on 9 February that she will challenge Düsseldorf’s ruling.
Speaking alongside the German Chancellor Angela Merkel, Ms Schavan said: “I will not accept this decision – I neither copied nor deceived in my dissertation.
“The accusations have hurt me deeply,” she told reporters.
She said she had taken the decision to step down from her post to protect it, the government and her political party from dishonour.
“If a research minister files a suit against a university, that of course places strain on my office, my ministry, the government and the Christian Democratic Union,” she said.
Her resignation follows the decision of a Düsseldorf academic panel, which announced on 5 February that it found Ms Schavan had plagiarised parts of her PhD thesis in philosophy, which focused on the formation of conscience.
Her departure comes two years after the-then minister of defence Karl-Theodor zu Guttenberg was stripped of his doctorate and quit when it emerged that he had copied large parts of his thesis.
Ms Merkel said she accepted Ms Schavan’s resignation “with a heavy heart”, saying she “has made her mark as the most acknowledged education expert in our country.”
Ms Merkel is due to fight parliamentary elections in September and attempt to secure a third term in office.
Ms Schavan’s decision was also met with respect by the political opposition.
Social Democrat leader Sigmar Gabriel said she has been a “highly honourable and competent colleague”, while Katrin Göring-Eckardt, a leading member of the Green Party said Ms Schavan’s case is “in a sense tragic.”
Ms Schavan will be replaced by Johanna Wanka, the outgoing regional education minister in the state of Lower Saxony, in north-west Germany.