Hours earlier, Trump said new strikes by Israel and Iran would not affect his administration's peace talks with Tehran, adding that Netanyahu "doesn't call the shots".
Trump has leaned on Israel to stop its attacks in Lebanon to allow room for a deal to end the wider war with Iran, including rebuking Netanyahu with obscenities in a phone call last week.
However, 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 fired a salvo of missiles at Israeli targets in retaliation, putting US-Iran peace talks at risk.
But Trump insisted that an agreement to end the wider war remains within reach.
"It's not going to have any impact on the deal," Trump told the Financial Times.
"I call the shots. I call all the shots. He (Netanyahu) doesn't call the shots."
A few hours later, Israel's defence forces said they had struck Iranian military targets.
Iran's Revolutionary Guards said Israel had carried out attacks on targets inside Iran using air-launched ballistic missiles.
The latest hostilities drove oil prices up more than three per cent in early trading on Monday, with benchmark Brent futures back above $US96 ($A136) a barrel.
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 and Netanyahu spoke by phone on Sunday, an Israeli official said.
Trump told Netanyahu to refrain from further strikes because "we are close to doing something good in terms of a deal", according to a US official quoted by Axios.
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 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.
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 attacked Israel since a ceasefire in the wider war started in April, although Hezbollah had.
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.
Israel has never 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 one-fifth of the world's oil. Washington has imposed its own blockade of Iranian ports.
Though Washington and Tehran have said they are close to a preliminary agreement that would reopen the strait, they have repeatedly traded strikes, with escalations in recent days that have included attacks on nearby Arab states hosting US bases.
with AP
