Ignazio Marino left his post as Mayor earlier in the week after leaving the capital amid rumours of corruption and debts.
He quit after the majority of his Councillors left his centre Left Democratic Party following a series of scandals.
Mr Marino was elected in 2013.
The Vatican had signaled that it was unhappy with the Mayor and a political website Dagospia reported that the Pope's Secretary of State Cardinal Pietro Parolin had mentioned to one of the Prime Minister's allies, Graziano Delrio: "Arrange for the Mayor to be dismissed," according to The Independent.
It has been reported that Mr Delrio had replied that this would not be possible.
A senior church figure, Monsignor Enrico Feroci, the director of Caritas in Rome says he "appreciated" that Mr Marino had resigned and that it had been unnecessary to "unblock a situation that had become negative for the city."
These claims come after a number of reports that have suggested Pope Francis did not see eye-to-eye with the Mayor on due to his outspoken support on gay marriage and his perceived failure, in the eyes of the Vatican, to prepare the city for the papal jubilee.
It has also been reported that Pope was not pleased that Mr Marino had falsely said he had been invited by the Vatican to join the Pope on his tour of America.
He also crashed one of the Pope's photos whilst wearing his Mayor sash.
If these claims are proved true it would falsify the belief that Francis does not involve himself in the politics of Rome.
The final straw came when Mr Marino had paid a number of restaurant bills with his city hall credit card.
He has promised to refund the €20,000 (around £15,000) from his own funds.
He will continue to run the city until a commissioner replaces him next year.
Speaking to La Stampa newspaper he said: "If it hadn't been for the receipts, sooner or later they'd have said that I have holes in my socks or they'd have planted cocaine in my pocket."
