"I have today submitted my resignation to the mayor who has with deep regret accepted it," he said.
The resignation will be seen as an embarrassing blow to Mayor Boris Johnson, coming less than a month after his deputy chief of staff was forced to resign after he made remarks regarded as disparaging about people from the Caribbean.
Johnson announced on Thursday he was launching an inquiry into media allegations of sexual and financial misconduct against Lewis, a Guyana-born ordained Church of England priest who runs a charity for black youths.
Lewis had dismissed the allegations as "complete rubbish" at a hastily arranged news conference with Johnson at his side at the Mayor's glass-clad City Hall office.
Johnson said he had every confidence in his deputy, but just over 24 hours later Lewis was back at the same briefing room announcing he was standing down.
"The inquiry ... has done little to calm the avalanche of allegations," he said.
"I cannot allow things that I have been in to, up to, and around me, to obscure the important business of this mayoralty and for that reason I must step down as Deputy Mayor for Young People with immediate effect."
Johnson had appointed Lewis to help tackle a wave of violent crime in London that has seen 18 teenagers die violent deaths this year, the latest a 16-year-old stabbed in south London.
"Today again we learn of another murder," said Lewis. "Yet so much time and attention has been given over to something that may or may not have happened 10 or 12 years ago -- and of course you know I flatly deny it."
The Church of England said on Thursday that Lewis had been barred from practising as a priest in England between 1999 and 2005 after working in the diocese of Chelmsford east of London in the 1990s.
Lewis said he was unaware of the ban.
Johnson, a member of the opposition Conservative Party, defeated long-serving mayor Ken Livingstone in May in a key loss for Prime Minister Gordon Brown's ruling Labour Party.
With the Conservatives running far ahead of Labour in national opinion polls, many observers see the way they perform in London as a litmus test of how they might perform in government. National elections must be held by mid-2010.