Al-Qaeda in the Arabian Peninsula (AQAP), seen by the United States as the global network's most dangerous franchise, has exploited Yemen's war to expand its presence in the country's south.
But the elite force, trained by the United Arab Emirates, on Thursday launched a "major operation" against the jihadists in Shabwa province.
The group staged a "tactical retreat" from the province with no major clashes, the military official said, requesting anonymity as he was not authorised to talk to the press.
Residents of an Abyan town near the Shabwa border said they counted at least 45 cars carrying armed AQAP militants through their district.
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AQAP's Shabwa stronghold has been a focal point in a long-running American-led drone war which has intensified since President Donald Trump took office in January.
A US air raid on the province in June killed AQAP emir Abu Khattab al-Awlaqi, according to the Pentagon.
Shabwa has also been the site of AQAP attacks in recent months, with the Yemen government reporting seven soldiers killed there in a suicide attack last week.
The UAE, part of a Saudi-led military alliance battling Iran-backed Huthi rebels in Yemen, said the operation was being "closely supported by a combined UAE and US enabling force".
Pentagon spokesman Navy Captain Jeff Davis said Friday that the operation involved "a very small number" of US forces on the ground whose main task was to help the flow of information.
The assault aimed to "degrade" AQAP's ability to coordinate terror attacks abroad, he said, adding that the US had conducted more than 80 strikes in Yemen since February 28.
More than 8,000 people have been killed in the Yemen war since Saudi Arabia and its allies intervened in 2015 to support the government against Huthi rebels who had seized the capital and swathes of the country's north.
Yemen also faces a deadly cholera outbreak and stands at the brink of famine.
The United Nations has called it "the largest humanitarian crisis in the world".