The cyberattack, which were approved by Trump on Thursday, targeted computer systems used to control missile and rocket launches that were chosen months ago for potential disruption, a US official familiar with the matter said on Saturday.
The strikes were carried out by US Cyber Command and in coordination with US Central Command, reports Efe news.
The official declined to provide specific details about the cyberattack, but said that it didn't involve loss of life and was deemed "very" effective.
The attack came during the peak of tensions this week between the US and Iran over a series of incidents across the Middle East, including Tehran's shooting down of an American reconnaissance drone.
It also came as US fears have grown that Iran may seek to lash out with cyberattacks of its own, as multiple cybersecurity firms said they had already seen signs Tehran is targeting relevant computer networks for intrusion and appeared particularly focused on the US government and the American energy sector, including oil and gas providers.
Cyber Command and the National Security Council didn't respond to requests for comment. Details of the cyber operations were first reported late Friday by Yahoo News.
Current and former US officials have warned that cyberattacks against Iran could increase the likelihood that Iran may respond in kind, and have noted Iran is particularly unpredictable in its own use of cyberattacks.
On Saturday, the Department of Homeland Security's top cybersecurity official, Chris Krebs, issued a statement warning that Iran's malicious cyber activities were on the rise.
Such attacks could be destructive in nature, Krebs said.
"What might start as an account compromise, where you think you might just lose data, can quickly become a situation where you've lost your whole network," he said.
The current concern about Iran's capabilities and intent builds on months of mounting alarm about how Iran could use cyber means to retaliate against the US for the Trump administration's tough posture and heated rhetoric toward the country, Dow Jones added in its report to EFE.
In April, the FBI issued an alert to private industry warning that Iran could retaliate in response to the US formally designating the Islamic Revolutionary Guard Corps as a terrorist organization.
The US attack on Thursday appear to be the first known instance of the US Cyber Command using new authorities granted by the president and Congress last year to more easily allow for disruptive cyber operations against other countries that didn't involve election security.
Previously, in a classified operation known as Synthetic Theology, US Cyber Command jammed servers belonging to the Internet Research Agency, a St. Petersburg, Russia, troll farm, according to people familiar with the operation.
White House National Security Adviser John Bolton, speaking earlier this month at a Wall Street Journal event, appeared to telegraph that these kinds of attacks would become more frequent.
"We're now opening the aperture, broadening the areas we're prepared to act in" beyond election security, Bolton said.
( With inputs from IANS )