Over 300 drones and missiles were fired at Israel overnight, which Iran said was in response to an 1 April strike on its consulate in Syria.
Almost all weapons were shot down by Israeli, US and allied forces before they reached their targets.
Officials said Joe Biden urged Israel to consider its response “carefully”.
Speaking to reporters on Sunday, a senior administration official said that Mr Biden told Israeli Prime Minister Benjamin Netanyahu to “think very carefully and strategically” about how his forces replied to the unprecedented action, the first direct attack by Iran on the country.
The official added that the Biden administration believes Israel “got the best of it” in the exchange, which began when senior Iranian military commanders were killed at an Iranian consular building in Syria.
About 99% of the missiles, drones and cruise missiles launched during Iran’s retaliatory operation were shot down or intercepted – which US officials point to as a sign of Israeli military superiority over Iran.
US aircraft and naval vessels shot down dozens of Iranian projectiles as the attack took place. More than 80 drones and at least six ballistic missiles were downed by US aircraft and vessels or by air defence forces over Iraq.
This includes seven drones and a ballistic missile as they prepared to launch from Yemen, US Central Command (Centcom) added in an update on Sunday.
A conversation took place between Mr Biden and Mr Netanyahu at a time “of heightened emotion” just after the attack, which included about 100 ballistic missiles simultaneously flying towards Israel.