"I have no evidence at this point from what I've seen that classified information was disclosed that in any way would have had a negative impact on our national security," Obama said in his first post-election news conference.
The former four-star general admitted last Friday that he had had an extramarital affair with a woman who was later identified as a co-author of his biography.
The FBI is also investigating Allen over his contacts with another woman whose complaints about anonymous, harassing e-mails led to the discovery of the Petraeus affair.
When asked if he should have known about the investigation into his former CIA chief earlier, the president said he is "withholding judgment" because all of the information is not yet available.
"I'm going to wait and see ... how this whole process unfolded," Obama added.
The scandal has threatened to complicate Obama's focus on critical negotiations with Congress over spending cuts and taxes.
It has also raised questions surrounding the CIA's response to congressional inquiries into the September terror attack on the U.S. diplomatic mission in Benghazi, Libya, that killed four Americans, including Ambassador Christopher Stevens.
On that matter, Obama offered a fierce defense of U.N. Ambassador Susan Rice, who has come under scrutiny for public comments in the days following the attack in which she placed blame for it on a mob enraged by an anti-Muslim video.
The president said Rice was speaking with the information provided by the intelligence community and has acted with "skill, professionalism, toughness and grace."
In response to statements Wednesday from Sen. John McCain and Sen. Lindsey Graham, who said they would block a potential Rice nomination for a Cabinet position, Obama said if the lawmakers want to "go after somebody, they should go after me. I'm happy to have that discussion with them."
"For them to go after the U.N. ambassador, who had nothing to do with Benghazi and was simply making a presentation based on intelligence that she had received, and besmirch her reputation is outrageous," he said.
On another pressing foreign policy issue, Obama said he was not ready to arm the Syrian opposition movement, saying that the nation needed to avoid indirectly providing weapons to groups or people who would seek to harm Americans or Israelis.
The United States is supporting a new coalition of Syrian dissidents and is seeking to accelerate assistance in their effort to force Syrian President Bashar al-Assad to leave office.
On budget matters at home, Obama opened the door to compromise regarding the impending fiscal cliff of tax increases and spending cuts.
The president said he was encouraged by recent comments from members of the Republican Party surrounding the need for more revenue from the wealthiest Americans as part of a plan to reduce the deficit.
"Both parties voted to set this deadline, and I believe both parties can make these decisions together ... in a balanced and responsible way," Obama said.
Obama stood by his previous statements about tax rates. He called on House Republicans to agree to Senate-passed proposals that would extend current tax rates for those making $250,000 a year while allowing rates to return to higher levels for those making over that amount and insisted he would not accept a lower tax rate for the wealthiest 2% of Americans.