Iran has long said any peace deal with the US would depend on a ceasefire also holding in Lebanon, which Israel invaded in March in pursuit of Iran-backed Hezbollah fighters who fired rockets and drones across the border in solidarity with Tehran.
But Israel earlier on Sunday launched strikes in the Beirut area for the first time since the US announced a truce plan for Lebanon last week.
Iran's Revolutionary Guards said they had targeted Ramat David air base, near Nazareth.
The Israeli military said it identified missiles launched from Iran and that its defence systems had intercepted them.
Trump, who was spending the weekend at his golf club in Bedminster, New Jersey, and Netanyahu spoke by phone for a little less than half an hour, an Israeli official said, without giving further details.
Earlier, Trump told news outlet Axios he would press Netanyahu not to retaliate.
"Israel had its strike and Iran had its strike. We don't need another one," Trump said.
"We are very close to a final deal with Iran. It is going to be a good deal. I don't want it to blow up because of what is happening now."
Israel would retaliate, said an Israeli source, speaking to Reuters on the condition of anonymity following the Iranian attack.
Shortly after midnight local time, the Israeli military issued a brief statement, citing Chief of Staff Eyal Zamir as saying his forces had not been directed to attack Iran so far, but would do so "with determination" once given the order.
Since the start of US-Iran talks aimed at halting the war, Israel has continued attacks in Lebanon in a conflict with Hezbollah that Israeli officials insist should be treated separately from any ceasefire with Iran.
Tehran demands that a peace deal with the United States include Lebanon, warning that Israeli attacks there were jeopardising talks.
Iran's chief peace negotiator, parliamentary speaker Mohammed Baqer Qalibaf, said US bases and Israeli assets are legitimate targets because of hostile acts, including the "violation of agreements over Lebanon".
Before Sunday, Iran had not targeted Israel since a ceasefire in the wider war started in April, although Hezbollah has done so.
Trump has repeatedly insisted that Washington and Tehran were close to an agreement on ending the war.
"We're very close to a deal, or I'm going to blow the hell out of them," Trump told NBC News' Meet the Press in a prerecorded interview that aired on Sunday to mark 100 days of the conflict.
Trump has leaned on Israel to stop its attacks in Lebanon to allow room for a peace deal with Iran, including rebuking Netanyahu with obscenities in a phone call last week. After that call, Netanyahu appeared to abandon plans to strike Beirut.
But Israel has never fully halted its Lebanon campaign, which has killed thousands of people and driven hundreds of thousands from their homes. Hezbollah, which did not take part in the truce talks, has also continued its attacks and says it will not give up its weapons unless Israel halts its attacks and withdraws from Lebanon.
Netanyahu said the Israeli strikes on Sunday on Beirut's southern outskirts, a district known as Dahiyeh that has long been a Hezbollah stronghold, were ordered in response to Hezbollah firing toward Israel.
The wider war has been stalemated since the US and Israel paused their attacks on Iran in early April, with Tehran blocking most shipping through the Strait of Hormuz, the main transit route for Middle East oil. Washington has imposed its own blockade of Iranian ports.
with AP and DPA
