Four vessels from Houthi-controlled areas in Yemen fired upon the Maersk Hangzhou and got within metres of the ship, the US military said.
Helicopters from nearby US warships responded to a distress call - and, after being fired upon, sank three boats "in self-defence".
The crews were killed and the fourth boat fled the area.
Houthi forces have been attacking ships in the Red Sea since November, launching more than 100 drone and missile attacks on vessels passing through the vital shipping lane.
The Iranian-backed Yemeni rebel group has previously claimed its attacks are directed at vessels linked to Israel, in response to the war in Gaza.
The commercial ship attacked, the Maersk Hangzhou, is registered to Singapore and operated and owned by a Danish firm, US Central Command (Centcom) said.
Maersk, one of the largest shipping companies in the world, says it has paused sailings through the Red Sea for 48 hours.
The firm had only resumed using the route a few days ago, after the US and its allies launched a mission to protect ships in the area.
Previously, its ships had diverted on a much longer route around the Cape of Good Hope because of the recent attacks on shipping.
The four Houthi boats attacked at around 06:30 Yemeni time (03:30 GMT) with mounted weapons and small arms, getting to within 20m (66ft) of the container ship, which the crew "attempted to board". The ships crew issued a distress call and a security team returned fire, Centcom said.
Helicopters from the nearby USS Eisenhower aircraft carrier and USS Gravely destroyer responded to the call for help and were shot at while "in the process of issuing verbal calls to the small boats".
The helicopters "returned fire in self-defence, sinking three of the four small boats, and killing the crews", Centcom said. It added that the fourth boat "fled the area" and no damage had been recorded to US personnel or equipment.
It was the second attack on the Maersk Hangzhou in 24 hours, after it was targeted with missiles on Saturday.
The anti-ship missiles were fired from Houthi-controlled areas and the destroyers Gravely and Laboon responded on Saturday, according to a previous Centcom statement.
A US Navy admiral told the AP news agency the missile attack was the first successful strike since a global patrol was launched on 18 December.
Centcom said while the ships were responding to the distress call, two anti-ship missiles were fired from Houthi-controlled areas at the pair of US navy vessels.
The USS Gravely destroyed the inbound ballistic missiles, Centcom said, adding it was the twenty-third "illegal attack by the Houthis on international shipping" since 19 November.
Centcom added the Maersk Hangzhou was "reportedly seaworthy and there are no reported injuries" on board.
Separately, the United Kingdom Maritime Trade Operations (UKMTO) organisation reported an incident in the Red Sea about 55 nautical miles (101km) to the south-west of the Yemeni port of Hodeidah.
The organisation said an unidentified ship had reported "a loud bang accompanied by a flash on the port bow of the vessel", and several explosions.
No damage was recorded and all members of the crew were reported unhurt, with the vessel escaping the area to a nearby port, the statement said.
| Update from the Times of Israel at 3:00 p.m. ET: |
At least 10 Iran's Houthi sock puppets
...a Zaidi Shia insurgent group operating in Yemen. They have also been referred to as the Believing Youth. Hussein Badreddin al-Houthi is said to be the spiritual leader of the group and most of the military leaders are his relatives. The legitimate Yemeni government has accused the them of having ties to the Iranian government. Honest they did. The group has managed to gain control over all of Saada Governorate and parts of Amran, Al Jawf and Hajjah Governorates. Its slogan is
God is Great, Death to Americaâ„¢, Death to Israel, a curse on the JewsThey like shooting off... ummm... missiles that they would have us believe they make at home in their basements. On the plus side, they did murder Ali Abdullah Saleh, which was the only way the country was ever going to be rid of him...
rebels were killed today and two maimed when US forces struck their boats in the southern Red Sea, two sources at Yemen
...an area of the Arabian Peninsula sometimes mistaken for a country. It is populated by more antagonistic tribes and factions than you can keep track of...
’s Hodeida port say.
The US military earlier said it had destroyed several small boats operated by the Iran-backed Houthis after the rebels attacked and tried to board a container ship.
One source at the rebel-controlled port says the maimed were rescued following the strike. The other source, also speaking on condition of anonymity
... for fear of being murdered...
, says there are four other survivors.