The 'Vanilla Sky' actors dated for three years in between his marriage to Nicole Kidman and Katie Holmes but reportedly split over Scientology.
While 38-year-old Penelope is now married and has a 19-month-old son named Leo with Javier Bardem with an adorable son Leo, 19 months, a new story that her previous relationship ended over Scientology.
Apparently Penelope refused to give up her own devout Buddhist beliefs.
The Oscar winner reportedly began the process of taking courses - and auditing sessions - in Scientology.
But Church leader and close confidante to Tom, David Miscavige, branded her a ''dilettante'' when he learned that she wouldn't give up her own religion.
The article claims, Tom's team of handlers began an auditioning process to find a suitable potential wife and hopefully a woman already enmeshed in the Church Of Scientology.
Former Scientologist Marc Headle told Vanity Fair magazine: ''It's not like you only have to please your husband - you have to toe the line for all Scientology. You can't do anything to displease Scientology, because Tom Cruise will freak out.''
The Church of Scientology strongly denied to Vanity Fair that any ''auditions'' ever took place, or that they objected to Penelope's religious beliefs.
In a statement to Us Weekly magazine they said: ''The allegations and entire premise of the Vanity Fair article related to Mr. Miscavige, the ecclesiastical leader of the Scientology religion, are totally unfounded and false and categorically denied. The statements and events described about the Church are denied in their entirety.''