Tina Beattie released a letter from the president of the Catholic school that said the invitation was being pulled because she dissents from church teachings.
University President Mary Lyons didn't elaborate in her letter but her decision came less than three months after Beattie and 26 other Catholics signed a letter in The Times of London newspaper that said it was "perfectly proper for Catholics, using fully informed consciences, to support the legal extension of civil marriage to same-sex couples."
University of San Diego officials had no immediate comment Friday.
"I hope you understand the difficulties associated with this decision, one to which I arrived with great and thoughtful consideration," Lyons wrote in a letter dated Oct. 27.
Pope Benedict XVI and Catholic leaders in the U.S. and around the world have been increasingly vigilant about ensuring that groups and individuals that operate in the name of the church are adhering to core Catholic teaching.
Beattie, a professor of theology and religious studies at Roehampton University, said the San Diego school rejected her plea to reconsider pulling the fellowship at its Frances G. Harpst Center of Catholic Thought and Culture. She blamed "a hostile minority of bloggers" for trying to discredit and distort her views.
Beattie wrote on her blog that she planned to steer clear of controversy in her San Diego lectures and seminars to avoid problems for her hosts in the "currently febrile atmosphere of American Catholic politics."
Gerard Mannion, the center's director, said he was "very surprised, shocked and deeply disappointed" by the university's decision. He said students and faculty were planning a series of protests.
In 2008, the University of San Diego withdrew its appointment of Rosemary Radford Ruether for serving on the board of an abortion rights organization, Catholics for Choice. Ruether had been named the Monsignor John R. Portman Chair in Roman Catholic Theology.