In his first public intervention into the crisis gripping America's security establishment, Mr Obama said there was "no evidence at this point, from what I have seen, that classified information was disclosed that would in any way have a negative impact on our national security".
He said Mr Petraeus "did not meet the standards that were necessary" of America's most senior spy by engaging in an extramarital affair with his biographer, Paula Broadwell, but moved to ease widespread fears that the infidelity may also have compromised secret information.
Mr Obama also defended the FBI's controversial decision to shield him and the public from its investigation into Mr Petraeus – which has ensnared another top US general – until after last week's election.
"The FBI has its own protocols in terms of how it proceeds," he said in a press conference at the White House, his first since winning re-election. "We are not supposed to meddle in criminal inquiries and that has been our practice."
Gen John Allen, the second married commander involved in the Petraeus scandal, received the backing of Leon Panetta, the US defence secretary, who said he had faith in the general's ability to lead allied troops in Afghanistan.
Gen Allen is accused of sending "flirtatious" messages to Jill Kelley (37), a Florida socialite embroiled in the scandal. Ms Kelley's complaint about harassing emails, which allegedly turned out to be from Ms Broadwell (40), prompted an FBI inquiry that unearthed the affair.
Speaking from Australia, Mr Panetta said: "He certainly has my continued confidence to lead our forces and to continue the fight."
The defence secretary also warned that "no one should leap to any conclusions" as Gen Allen continued to deny any inappropriate behaviour with Ms Kelley.
Sources close to the general reject reports that his correspondence with Ms Kelley amounts to tens of thousands of pages, and say that the messages contain nothing more incriminating than affectionate language between friends such as "sweetheart".
However, one defence official is reported to have told Fox News that some of the emails between the pair were indeed sexually explicit, describing them as the "equivalent of phone sex".
The crisis developed after Ms Kelley was allegedly bombarded with anonymous threatening emails warning her off Mr Petraeus, and decided to lodge a complaint with a contact at the FBI.
This prompted the inquiry that would lead to Mr Petraeus's resignation as CIA director and implicate Gen Allen. (© Daily Telegraph, London)