Militants fled to nearby mountains after the clashes in Al-Hawtah district of Shabwa province, said a Yemeni officer, declining to be named.
He said Apache helicopters belonging to the United Arab Emirates (UAE) -- a key member of a Saudi-led Arab coalition in Yemen -- then strafed the mountains where the jihadists had fled.
"We entered Al-Hawtah after clashes with the terrorists and now we're stationed in several locations... We are in total control of the area," the officer said.
Al-Qaeda has flourished in the chaos of Yemen's civil war and in August, Emirati-trained Yemeni special forces launched a US-backed operation against the group, also the target of a long-running US drone campaign.
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Yemeni forces have brought Shabwa province largely under government control, though Al-Qaeda is known to make tactical retreats to mountain refuges, only to resurface.
Despite the coalition intervention on behalf of President Abedrabbo Mansour Hadi, his government's authority is still largely confined to Yemen's south and areas along the Saudi border.
The Huthis on Tuesday threatened to attack ports and airports in the UAE and Saudi Arabia in response to a tightened blockade of Yemen enforced by the coalition.
The war gripping Yemen has killed more than 8,650 people since the coalition intervention began.
Unless the blockade is eased, Yemen could experience the world's worst famine in decades, the United Nations has warned.