He said Iran and the rest of the region should know that “if anybody messes with Israel, America will be there”.
But he rejected a call by Israeli PM Benjamin Netanyahu that any deal be conditional on Iran recognising Israel.
Mr Obama said such a condition would be “a fundamental misjudgement”.
The president, speaking in an interview with National Public Radio, said that it would be akin to saying the US would not seal a deal unless the Iranian regime completely transformed.
“We want Iran not to have nuclear weapons precisely because we can’t bank on the nature of the regime changing. That’s exactly why we don’t want to have nuclear weapons,” he said.
“If suddenly Iran transformed itself to Germany or Sweden or France, then there would be a different set of conversations about their nuclear infrastructure.”
On Monday, President Obama also sought to reassure Oman about the effects of a nuclear deal with Iran.
In a phone call, he told Sultan Qaboos that the US would work “with Oman and other regional partners to address Iran’s destabilising activities in the region”.
‘Right to be concerned’
Critics have accused President Obama of conceding too much ground to Iran and endangering Israel’s security.
But in an interview with the New York Times, Mr Obama firmly denied this.
“I would consider it a failure on my part, a fundamental failure of my presidency, if on my watch, or as a consequence of work that I had done, Israel was rendered more vulnerable,” he said.
Mr Obama said he recognised the concerns raised by Israeli Prime Minister Benjamin Netanyahu, a fierce critic of the deal along with the president’s Republican opponents in the US Congress.
He said Israelis “have every right to be concerned about Iran”, a country that had threatened “to destroy Israel, that has denied the Holocaust, that has expressed venomous anti-Semitic ideas”.
But he insisted that the preliminary agreement with Iran – a forerunner of a comprehensive deal, due to be agreed before 30 June – was a “once in a lifetime opportunity” to curb the spread of nuclear weapons in the Middle East.
Under the terms reached last Thursday, Iran must slash its stockpile of enriched uranium that could be used in a nuclear weapon, and cut by more than two-thirds the number of centrifuges that could be used to make more.
In return, UN sanctions and separate measures imposed unilaterally by the US and EU will be gradually suspended as the global nuclear watchdog, the International Atomic Energy Agency (IAEA), confirms Iranian compliance.
Speaking on Sunday on CNN, Mr Netanyahu said: “Not a single centrifuge is destroyed. Not a single nuclear facility is shut down, including the underground facilities that they build illicitly. Thousands of centrifuges will keep spinning, enriching uranium. That’s a very bad deal.”
But Senator Lindsey Graham of South Carolina, a possible Republican presidential candidate, said it was “probably the best deal that Barack Obama could get with the Iranians” and that he would wait to see how the final agreement looked before passing judgement.
“I don’t mind giving the administration the time between now and June to put this deal together,” he told CBS.