The University of Duesseldorf's philosophy faculty decided on Tuesday that she had carried out "a deliberate deception through plagiarism".
The minister has denied the claims and said she will appeal.
An earlier plagiarism row brought an end to the political career of Germany's defence minister in 2011.
Large parts of Karl-Theodor zu Guttenberg's 2006 legal dissertations were found by Bayreuth University to have been copied and he stood down before it issued its damning verdict in May 2011.
Using the same words as Duesseldorf's Heinrich Heine University, it concluded that he had "deliberately deceived".
When Ms Schavan became the second minister in Chancellor Angela Merkel's government to be accused of copying her doctorate, in this case by an anonymous blogger, she insisted she had never "knowingly falsely cited any sources" and promised to respond to the accusations.
But the faculty committee concluded that her work, which dealt with the formation of conscience, included a "substantial number of unaccredited direct quotes from other texts".
In a statement declaring the doctorate invalid and withdrawing it from Ms Schavan, the faculty head Bruno Bleckmann said they had "decided by secret ballot, by 12 votes to two, with one abstention".
The minister herself, 57, was said to be on a five-day education and science co-operation trip to South Africa.. Education minister since 2005, she is described as a close colleague of Chancellor Merkel.
Her lawyers reportedly rejected the university's ruling and said Ms Schavan would appeal.
When the university announced its inquiry, she said she had no intention of standing down.
But the investigation into one of Chancellor Merkel's closest allies is seen as potentially awkward months before Germans vote in federal elections.
The popular German newspaper Bild said the news was a bitter blow to the chancellor, and wondered whether she would need to find a new education minister at the start of her election campaign.
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