The studio declined to give further details or say who would replace the 24-year-old actress.
Fox, notorious for making attention-grabbing comments to the media, engaged in a public spat with director Michael Bay around the release of part two last summer. But Bay later defended her and said he looked forward to working with her on part three.
"Transformers" from 2007 and the 2009 sequel "Transformers: Revenge of the Fallen" have made more than $1.5 billion worldwide. According to Paramount, production is scheduled to begin this month on the third installment, with a release date set for July 1, 2011.
The Associated Press contributed to this report.