The UAE had no immediate reaction to the claim, which further escalates tensions between the neighbouring nations on the Arabian Peninsula as their partnership in the years-long war in Yemen breaks down.
A Saudi military statement claimed Aidarous al-Zubaidi, the leader of the Southern Transitional Council, fled Yemen by boat to Somalia.
Then, UAE officials flew al-Zubaidi to Abu Dhabi, the capital of the Emirates, the statement said on Thursday.
The UAE has been the major supporter of the council, known as the STC, which sparked a confrontation between Saudi Arabia and the Emirates in recent days after STC fighters advanced in two governorates and appeared to be preparing to secede from Yemen.
The Saudi statement from Major General Turki al-Malki included him naming a major general in the UAE as being involved in al-Zubaidi's alleged escape, along with identifying his nom de guerre, something highly unusual in the typical clubby world of Gulf Arab relations.
It also suggested an Ilyushin Il-76 aircraft used in the operation had been used in "conflict zones" such as Ethiopia, Libya and Somalia - routes the Emirati military has been accused of funnelling weapons through in the past.
The UAE denies running guns into those areas.
The Emirati foreign ministry did not immediately respond to a request for comment.
The STC did not immediately acknowledge the allegation, either, saying al-Zubaidi had remained in Aden, where forces allied against the Iranian-backed Houthi rebels had congregated for years since the rebels seized Yemen's capital, Sanaa.
Southern Yemen had been run under the Presidential Leadership Council, a group including al-Zubaidi and others, since 2022.
On Wednesday, the leadership council expelled al-Zubaidi and charged him with treason after he apparently declined to fly to Saudi Arabia for talks.
It marked the latest pushback against the STC by Saudi Arabia, which also recently launched air strikes against the group and an arms shipment the kingdom said came from the UAE.
The war in Yemen has killed more than 150,000 people, including fighters and civilians, and created one of the world's worst humanitarian disasters.
The Houthis have also launched attacks against shipping over the Israel-Hamas war in the Gaza Strip, disrupting a vital route for global commerce.
The US, which earlier praised Saudi-Emirati efforts to end the crisis over the separatists, has launched air strikes against the Houthi rebels under both Presidents Joe Biden and Donald Trump.
Saudi Arabia's foreign minister met US Secretary of State Marco Rubio in Washington on Wednesday.
This latest accusation will further strain ties between Saudi Arabia and the UAE, OPEC members and neighbours that increasingly have competed over economic issues and regional politics, particularly in the Red Sea area.
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