The missiles were fired at the USS Mason from Houthi-controlled territory in war-torn Yemen, Capt. Jeff Davis said, adding that the guided-missile destroyer
deployed "onboard defensive measures" and was undamaged.
But the Houthis -- a minority Shia group that has taken control of much of Yemen, including the capital -- denied Monday that its forces had targeted the warship.
An official from the Houthi-controlled military said the reports were aimed at covering up a "heinous" Saudi-led coalition airstrike on a wake Saturday in the capital, Sanaa, that officials said killed at least 155 people, the Houthi-controlled SABA news agency reported.
"Reports that allege that Yemeni rockets targeted ships off the Yemeni (coast) are baseless," the official said.
The US warship was in international waters more than 12 nautical miles (22 km) offshore, in the southern end of the Red Sea, north of the Bab el-Mandeb Strait, according to a defense official.
The missiles were launched within 60 minutes of each other, Davis said.
"We assess the missiles were launched from Houthi-controlled territory in Yemen. The United States remains committed to ensuring freedom of navigation everywhere in the world, and we will continue to take all necessary steps to ensure the safety of our ships and our service members," he said.
Airstrike on wake
Washington has backed a Saudi-led coalition fighting to prevent Houthi rebels
allied with Iran and forces loyal to Yemen's deposed President Ali Abdullah Saleh from taking power in Yemen.
But on Saturday the US said it was reevaluating its support after the deadly wake airstrike.
The Saudi-led coalition had earlier denied accusations that it was responsible for the attack
and said it would "immediately investigate" reports that its warplanes were behind the airstrikes, according to the official Saudi Press Agency.
How war broke out
The Saudi-led coalition, involving several Arab countries,
began a military campaign in Yemen in March 2015 after Houthis drove out the US-backed government, led by President Abdu Rabbu Mansour Hadi, and took over Sanaa.
The crisis quickly escalated into a multisided war,
which allowed al Qaeda and ISIS -- other enemies of the Houthis -- to grow stronger amid the chaos.
Since peace talks in Kuwait failed in August, the coalition has intensified airstrikes, despite vocal criticism from rights groups that the bombardments have been indiscriminate and could constitute war crimes. The attacks have often hit civilian targets with devastating results.
The United States has come under increasing pressure to stop selling arms to Saudi Arabia.
The US Senate last month rejected a bipartisan proposal to block a pending $1.15 billion United States arms sale
Critics of the military deal, which was approved by the Obama administration, complained it could further drag the US into the war in Yemen and contribute to the worsening humanitarian crisis there.
Civilian casualties are only part of the crisis. Yemen's UNICEF office has reported that nearly 10,000 children younger than 5 died from preventable diseases there during the past year.
Some 1.5 million children are currently malnourished in Yemen, and 370,000 of them suffer from severe acute malnutrition, according to the charity.
Yemen's economic infrastructure has also been ravaged by war.
At least 430 factories and companies were destroyed by coalition airstrikes since the start of the conflict, according to Ahmed Bahri, political chief of the Sanaa-based Haq Party.