The couple, both 22, held a religious ceremony at La Cervara, a converted monastery near Genoa, despite being warned by the local bishop's office against the plan.
The bishop's office told the Rooneys that La Cervara is deconsecrated and not suitable for a wedding.
It suggested a different church, five miles away.
A five o'clock time slot had even been pencilled in at San Michele di Pagana by the curia.
Nevertheless, the couple ignored the advice and Father Edward Quinn, their local priest from Croxteth, presided over a ceremony in which rings were exchanged.
The wedding party dined on hamburgers and lobster, washed down with champagne.
Father Mario Ostigoni, the priest in charge of the marriage office, warned: "If the marriage was celebrated at La Cervara, then it is invalid in the eyes of the Church, ipso facto."
He added: "The bishop did not give his permission, so it was not a wedding. Even a prayer or blessing would be considered very inappropriate."
Father Ostigoni said that if the staunchly Catholic couple wanted a real wedding, they would have to have another ceremony.
"They were given the opportunity to celebrate both a civil and religious wedding. What they decided to do does not make much sense and is sad, because marriage should be a public declaration," he said.
"Now, respecting the privacy of the spouses, I can say that they should carry out a religious wedding elsewhere."
The local church will also launch an investigation into how the celebration was performed without permission.
However the couple's spokesman said: "They are definitely married, legally and in the eyes of the church. This was a meticulously planned wedding."
The couple had a civil marriage at Villa Durazzo, a 17th century palace at Santa Margherita Ligure, before the religious ceremony.
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