Duesseldorf’s Heinrich Heine University voted last Tuesday to remove her doctorate following a review.
Annette Schavan, a close ally of Chancellor Angela Merkel, had insisted she would fight the ruling and not resign.
In 2011, Defence Minister Karl-Theodor zu Guttenberg also quit after allegations he plagiarized his thesis.
Annette Schavan, 57, was awarded her doctorate 30 years ago, but the university found she had “systematically and intentionally” copied parts of it.
She had been scathing in her criticism of Karl-Theodor zu Guttenberg when the scandal of his plagiarism broke.
Analysts say her resignation will be hugely embarrassing to Angela Merkel.
Angela Merkel is facing federal elections on September 22.
Part of Annette Schavan’s brief as education minister is to oversee German universities.
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