Sister Catherine Rose Holzman was 89.
She was one of two nuns locked in a legal battle with Perry and the Los Angeles Archdiocese over a former convent in the city.
Perry agreed to buy the property for $14.5m (£10.4m) in 2015, but the deal turned sour when the former residents objected.
Sister Catherine Rose and Sister Rita Callanan said they were uncomfortable handing the convent and its eight surrounding acres over to the star, whose sometimes provocative hits include I Kissed A Girl and Ur So Gay.
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