Donald Trump said Israel had already launched retaliatory strikes against Iran before his call for restraint.
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The US president insisted if he tells the Israeli prime minister Benjamin Netanyahu to do something “he does it”, after he appeared to ignore Mr Trump’s demand to hold back from responding militarily.
In a phone interview with the BBC, Mr Trump said he stressed the need “to use a lot of common sense” when he spoke to the Israeli leader, amid ongoing negotiations aimed at securing an end to hostilities.
He made his comments as Iran and Israel committed conditionally to halting attacks after the two sides exchanged fire for the first time since the April truce, threatening to plunge the Middle East back into full-scale war.
He had earlier urged both countries to “immediately stop shooting”.
Israel attacked Iran after Tehran fired missiles towards Israel late on Sunday, which it said were in response to Israeli strikes on Lebanon.
Despite the renewed clashes, Mr Trump insisted talks on a potential peace deal were progressing “subject to ignorance or stupidity getting in its way”.
In his call with Mr Netanyahu, Mr Trump told the BBC: “All I did is say, ‘we have to use sense’. We’re very close to signing a very powerful deal, a very good deal.
“No nuclear weapons, no nothing. You know, we have to use a lot of common sense. It was fine.”
On Mr Netanyahu firing missiles against Iran, despite the president’s request not to, Mr Trump said: “No, no. They had already gone. They had already gone. They were already on their way.”
Mr Trump added: “If I tell him to do something, he does it.”
Meanwhile, Sir Keir Starmer said he was “deeply concerned” following the latest outbreak of violence in the region which sent oil prices soaring.
The Prime Minister said: “There are serious negotiations going on towards a lasting peace.
“It’s really important that we give them every chance of success because this conflict is already having a huge impact across the world, including here in the United Kingdom.
“So I say to all parties, we all have a responsibility to get back to that ceasefire and it’s really important we’re very clear about that.”
Announcing an end to its offensive, Iran’s military joint command said it had “delivered a painful response” to Israel for its attacks on Lebanon.
But it warned further “aggression and hostile acts” would mean “much more severe and crushing measures than before will follow”.
Mr Netanyahu has also said “right now, the fire has been halted”, but stressed Israel’s right to self-defence, pointing out he said this “with appreciation and respect in my good conversations with my friend President Trump”.
He warned if Iran “makes the mistake and returns to attacking us, we will respond with force”.
Against this volatile backdrop, Iran’s ambassador to the United Nations Amir-Saeid Iravani said he hoped a deal with the US could be reached by the end of June.
He said: “We have not received to a final document, but we are pursuing to receive it.”