Helicopters from the USS Eisenhower responded to a second distress call from a Danish container ship in 24 hours.
US Navy destroys Houthi “small boats” trying to board a container ship in the Red Sea.
The US military said four ships from Houthi-controlled areas in Yemen opened fire on the Maersk Hangzhou and came within meters of the ship.
Helicopters from nearby US warships responded to a distress call – and, after being fired upon, sank three boats “in self-defense”.
The crew were killed and the fourth boat fled the area.
A Houthi spokesman said the ship had refused to respond to alarm calls and 10 of its crew members were dead or missing after the incident.
Houthi forces have been attacking shipping in the Red Sea since November, launching more than 100 drone and missile attacks on ships passing through the main shipping lane.
An Iran-backed Yemeni rebel group has previously said the attack on ships bound for Israel was in retaliation for the war in Gaza.
The targeted merchant vessel, the Maersk Hangzhou, was registered in Singapore and owned and operated by a Danish company, US Central Command (Centcom) said.
Four Houthi boats attacked at 06:30 Yemen time (03:30 GMT) with loaded weapons and small arms, within 20m (66 feet) of the container ship, where the crew “attempted to board”. Centcom reported that the ship's crew issued a distress call and a security team opened fire.
The nearby USS Eisenhower aircraft carrier and USS Gravely destroyer helicopters responded to the call for help and were fired upon “on a mission to deliver verbal calls to small boats”.
The helicopters “returned to defend themselves, sinking three of the four small boats, killing the crew”, Centcom said. It said the fourth boat had “left the area” and that there was no damage to US personnel or equipment.
It was the second attack on Hangzhou in 24 hours, after targeting the ship on Saturday. CENTCOM said anti-ship missiles were fired from Houthi-held areas and the destroyers Gravely and Laboon retaliated.
Maersk said the attack happened around 17:30 GMT. It confirmed that its ship was “hit by an unknown object” but “there was no sign of fire on board”.
Maersk, one of the world's largest shipping companies, has suspended sailing through the Red Sea for 48 hours.
The company only started using the route a few days ago after the US and its allies began protecting ships in the area.
Earlier, recent attacks on shipping led to its ships being diverted on the longest route around the Cape of Good Hope.
A US Navy admiral told the AP news agency that Saturday's missile strike was the first successful strike since the global patrol began on December 18.
CENTCOM reported that two anti-ship missiles were fired at US Navy ships from Houthi-controlled areas as the ships responded to the distress call.
The USS Gravely destroyed incoming ballistic missiles, the twenty-third “unlawful attack” by the Houthis on an international vessel since November 19, Centcom said.
Centcom said the Maersk Hangzhou was “reportedly seaworthy and there were no injuries”.
Separately, the United Kingdom Maritime Organization (UKMTO) reported an incident in the Red Sea 55 nautical miles (101 km) southwest of the Yemeni port of Hodeidah.
The organization said an unidentified ship reported “a loud bang with a flash on the port bow of the ship” and several explosions.
No damage was reported and all crew members were reported unhurt, the report said, adding that the vessel had fled the area to the nearest port.
The escalation of Houthi attacks over the past several weeks has led several shipping companies, including Maersk, to divert their ships from the Red Sea – sailing around the Horn of Africa instead.
To reach Egypt's Suez Canal – which connects it to the Mediterranean Sea – ships must pass through the tiny Bab al-Mandab Strait, just off the coast of Houthi-controlled areas in Yemen.
The Iranian-backed rebels have previously said they would only target merchant ships “connected to Israel” in response to the war in Gaza, saying the attacks were an attempt to halt Israeli attacks on Palestinians.
In a statement on Sunday, UK Foreign Secretary David Cameron told Iran's foreign minister that Tehran “shares responsibility for preventing these attacks by providing long-term support to the Houthis.”
WATCH: Yemen's Houthis released video in November showing gunmen taking down a cargo ship from a helicopter.
In an interview with the AP, U.S. Navy Vice Admiral Brad Cooper said the Houthis do not appear to be ending their “irresponsible” attacks, in light of a new maritime task force designed to combat them.
Earlier in December, the US launched Operation Prosperity Guardian – an international coalition to protect shipping in the region.
Vice Adm. Cooper added that 1,200 merchant ships have passed through the Red Sea since the operation began, and none had been hit by drone or missile strikes as of Saturday.
The US Department of Defense said the Houthis had carried out more than 100 drone and ballistic missile strikes since November after the international task force was notified. The attack attempts targeted 10 merchant ships connected to more than 35 different countries, it added.
The Red Sea is one of the world's most important shipping lanes because it connects the markets of Europe with Asia.
Analysts have warned that the attacks could send prices soaring as it is one of the most important routes for exports of oil and liquefied natural gas produced in the Middle East.
