Three aircraft delivered food and water and left the drop zone after 15 minutes, according to the Pentagon.
Mr Obama said he had agreed to targeted strikes, if needed, to protect US citizens working in Irbil, and also to prevent a potential “genocide” of the Yazidi people.
He stressed there was no intention of sending in any troops.
Downing Street said there would be no military action in Iraq.
A spokeswoman said Downing Street welcomed the action taken by the US but added: “We are not planning a military intervention.”
The US announcement, threatening a renewal of US military involvement in the country’s long sectarian war, came amid fears of a humanitarian crisis.
Some 40,000 residents from the ancient Yazidi community have been forced to leave the northern Iraqi town of Sinjar after Sunni fighters overwhelmed Kurdish forces.
Many of them are trapped on Mount Sinjar without food or water and are at risk of starvation as Islamist militants surround the base.
“Today I authorised two operations in Iraq,” said President Obama.
“Targeted airstrikes to protect our American personnel and a humanitarian effort to save thousands of Iraqi civilians.”
The president said the military would act to stop the advance on Irbil by The Islamic State, the group previously known as ISIS or ISIL.
The US has a consulate in the city, where civilian and military staff work.
Militants have been surging across the north of Iraq towards Irbil, the capital of the Kurdish region.
“I’ve directed our military to take targeted strikes against ISIL convoys, should they move toward the city,” said President Obama.
“We intend to stay vigilant and take action if these terrorist forces threaten our personnel or facilities anywhere in Iraq.”
Two F-18 fighter jets kept watch over the three cargo aircraft, one C-17 and two C-130s – during the Mount Sinjar aid mission.
The planes dropped 72 bundles, containing more than 20,000 litres of drinking water and 8,000 pre-packaged meals.
President Obama said the Iraqi government had asked the US for help, with as many as tens of thousands hiding in the mountains with “little but the clothes on their backs”.
“Children are dying of thirst, meanwhile ISIL forces have called for the destruction of the entire Yazidi people, which would constitute genocide,” the President said.
“These innocent families are faced with a horrible choice: Descend the mountain and be slaughtered, or stay and slowly die of thirst and hunger.”
Airstrikes had been approved to help Iraqi forces and stop a “massacre” of the Yazidis, said the US leader.
The Islamic State has issued the Yazidi people an ultimatum to convert to Islam, pay a religious fine, flee their homes or face death.
It sees the Yazidis, who are followers of a religion derived from Zoroastrianism, as “devil worshippers”.
Attacks on minorities in Iraq could constitute a crime against humanity, said the UN Security Council at an emergency meeting on Thursday.
Hundreds of thousands of people, mostly Christians, are fleeing from the jihadists who have swept through more than a dozen towns in recent days.
Among them, the militants captured Iraq’s biggest Christian town, Qaraqosh, prompting many residents to leave, fearing for their lives.
The group has declared a caliphate, an Islamic state, across much of Iraq and Syria and wants to bring in a strict version of Islamic law.