Senior US officials said they had received assurances from Tehran that the crews -- taken to Farsi Island -- would be allowed to sail onwards come first light.
But the embarrassing crisis continued as President Barack Obama gave his last State of the Union address, undermining any attempt to cite closer relations with Tehran as part of his legacy.
Iran's Revolutionary Guards confirmed that the two boats and 10 personnel "were seized by combat units of the Guards naval force and moved to Farsi Island."
The force said the US personnel -- nine men and one woman -- were in good health and being treated in an "Islamic manner" in an "appropriate location."
US Secretary of State John Kerry called his Iranian counterpart Foreign Minister Mohammad Javad Zarif, with whom he negotiated the Iran nuclear deal.
As Kerry arrived at the Capitol to hear Obama's speech, he told a CNN reporter the sailors would be freed "very soon."
Washington has no diplomatic relations with Tehran, but Kerry and Zarif forged a bond during the long talks over the pact and remain in regular contact.
"He has a close relationship with foreign minister Zarif and that would be a natural point of contact," White House communications director Jen Psaki told CNN.
"We have been in touch with the Iranians. We have been assured of their safety and that they will be able to move forward on their journey promptly," she said.
"Obviously, any situation like this we take very seriously, and that's why we acted very quickly to get in touch and determine as much as we can."
A US defense official, speaking on condition of anonymity, said one or both of the vessels -- small patrol boats -- may have had a "mechanical incident."
Farsi Island lies in the Gulf, roughly midway between Iran and Saudi Arabia, and houses a base of Iran's Republican Guard Corps, which has its own naval units.
The tiny territory extends Iranian waters deep into one of the world's most important shipping lanes, an oil superhighway and potential flashpoint.
"Earlier today, we lost contact with two small US naval craft en route from Kuwait to Bahrain," a senior US administration official said.
- Oil superhighway -
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American officials did not dispute that the vessels appeared to have been in Iranian territorial waters when they were intercepted by Tehran's forces.
The vessels were said by US officials to be "riverine patrol boats" under 65 feet (20 meters) in length.
The Iranian news agency FARS said they were armed with three machine guns and that their onboard GPS confirmed they had been in Iranian waters when taken.
"At this early stage," another senior administration official said, there is "nothing to indicate" that Iran had committed a hostile act.
Ben Rhodes, a top national security aide for Obama, said the administration was "hopeful we will be able to resolve the issue."
The nuclear accord foresees Iran scaling back its nuclear program to put a bomb outside its reach in exchange for relief from international sanctions.
The deal is to be implemented very soon -- Kerry has said "in the coming days" -- but has been criticized by Obama's US opponents as too soft on Tehran.
These rivals seized on the incident in the Gulf to hammer on this point, demanding Obama make a statement and warned Iran must release the sailors.
"Iran is testing the boundaries of this administration's resolve," Republican presidential hopeful Marco Rubio said.
"You are only seeing this accelerate since the deal was signed with Iran," he added, warning he would repeal the deal if elected to the White House.
- Regional tensions -
The situation has been further complicated in the New Year by an angry breakdown in relations between Iran and US ally Saudi Arabia, inflaming regional tensions.
Iran's hardline Revolutionary Guard often takes a tough approach to perceived and real territorial violations in what it considers the "Persian Gulf."
Last year, Iranian patrol boats seized the Maersk Tigris, a cargo ship sailing under the Marshall Islands flag, which meant it was under US protection.
And in March 2007, Iranian patrols captured 15 British Royal Navy and Royal Marines personnel, interrogated them and held them for 13 days before releasing them.