The University of Dusseldorf faculty council voted 12-2 Tuesday to take away Schavan's doctorate. As she had done earlier, Schavan, who is appealing the school's decision, denied the allegations she plagiarized her doctoral dissertation, Der Spiegel reported.
"I will not accept the university's decision," she said. "I neither copied nor deceived."
Chancellor Angela Merkel was at her side when she made her announcement, the magazine said.
"Annette Schavan offered me her resignation last night," Merkel said, adding she accepted it with deep regret. "She knows that brains are the capital of people in this country. And she knows that good study conditions are just as important as promoting excellence."
Schavan thanked Merkel "for your words today and your friendship."
Merkel picked Johanna Wanka, an education minister in Lower Saxony state, to replace Schavan.
The university said Schavan "systematically and deliberately presented intellectual efforts throughout her entire dissertation that were not her own" with large sections taken from elsewhere without adequate attribution. Schavan, the university said, was guilty of "intentional deception through plagiarism" when she submitted the work 30 years ago.
Schavan is the second member of Merkel's Cabinet to be felled by plagiarism allegations. In 2011, Defense Minister Karl-Theodor zu Guttenberg left after being found to have plagiarized large sections of his doctoral thesis.