A spokesman for Mr Cameron said: "David fully supports Boris's decision.
"He has acted quickly and fairly in dealing with this unfortunate and difficult matter."
The allegations against Mr Lewis date back to his time as a vicar in the Parish of St Matthew in West Ham, east London, in the late 1990s.
They include claims that he received money from a man with learning difficulties and owed a debt to a fellow priest.
In a third case, a female parishioner went to church authorities and the police after giving Mr Lewis £25,000 to invest for her.
She started receiving regular interest payments but these allegedly stopped after a few months.
And Mr Johnson said his confidence in Mr Lewis was shaken after he discovered he was not a "fully-fledged" magistrate.
London's deputy mayor for policing has said the fight against knife crime will go on
Kit Malthouse, London's deputy mayor for policing, said it was "ungracious" for Labour to "dance on the political grave" of someone who had dedicated himself "to saving young lives in London".
He said: "It's very sad he's had to go because of questions which are being asked about his past, but the truth is he went because the story was becoming him and distracting from the work we've done."
Mr Malthouse said the battle against knife crime in London would carry on despite Mr Lewis's departure.
'Shoulder to shoulder'
At a news conference with his deputy at City Hall on Thursday, Mr Johnson announced an inquiry would be launched into the allegations which he said should not stop Mr Lewis from serving in his role.
However, Mr Johnson later said his "confidence was shaken" when he was wrongly led to believe that Mr Lewis, the deputy mayor for young people, was a magistrate.
Ms Blears said: "Boris Johnson stood shoulder to shoulder with Ray Lewis but he has followed Boris's deputy chief of staff and become the second senior resignation from the Boris Johnson mayoral team in recent weeks.
"Londoners need to know what Boris knew and why the situation has changed."
Ken Livingstone, who was replaced by Mr Johnson as London Mayor, said: "In my entire eight years in office I suffered only one enforced resignation of any of my most senior officials, Lee Jasper, and that only after seven years.
"This extreme contrast shows vividly the incompetence of Boris Johnson and his administration.
"It is an equal crisis for David Cameron who, it should be remembered, chose to make his first photo opportunity as Tory leader with Ray Lewis."
Mr Johnson said he accepted Mr Lewis's resignation with "extreme reluctance".
In a statement he added: "I cannot deny, however, that my confidence in Ray was shaken by the discovery today that he is not a fully fledged Justice of the Peace and I cannot deny that to be misled on this issue has made it harder for me to give Ray the backing necessary to continue in his role as Deputy Mayor."
Mr Lewis said he had been recommended as a magistrate but he had not been appointed as one.
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