The kingdom later directly linked the UAE to the separatists' recent advances in Yemen and on Tuesday warned Abu Dhabi its actions were "extremely dangerous".
The attack signals a new escalation in tensions between the kingdom and the separatist forces of the Southern Transitional Council, which is backed by the Emirates.
It also further strains ties between Riyadh and Abu Dhabi, which had been backing competing sides in Yemen's decade-long war against the Iranian-backed Houthi rebels amid a moment of unease across the wider Red Sea region.
The two nations, while closely aligned on many issues in the wider Mideast, increasingly have competed with each other over economic issues and the region's politics.
Yemen's anti-Houthi forces later declared a state of emergency on Tuesday, ending its co-operation with the UAE and ordering all Emirati forces within its territory to leave within 24 hours.
It issued a 72-hour ban on all border crossings in territory they hold, as well as entries to airports and seaports, except those allowed by Saudi Arabia.
A military statement carried by the state-run Saudi Press Agency announced the strikes, which it said came after ships arrived there from Fujairah, a port city on the UAE's eastern coast.
"The ships' crew had the disabled tracking devices aboard the vessels, and unloaded a large amount of weapons and combat vehicles in support of the Southern Transitional Council's forces," it said.
"Considering that the aforementioned weapons constitute an imminent threat, and an escalation that threatens peace and stability, the Coalition Air Force has conducted this morning a limited air strike that targeted weapons and military vehicles offloaded from the two vessels in Mukalla."
It was not immediately clear if there were any casualties from the strike or if any other military besides Saudi Arabia's took part.
The Saudi military said it conducted the attack overnight to make sure "no collateral damage occurred".
The UAE did not immediately respond to a request for comment from the AP.
Mukalla is in Yemen's Hadramout governorate, which the Council had seized in recent days.
The port city is some 480km northeast of Aden, which has been the seat of power for anti-Houthi forces in Yemen after the rebels seized the capital, Sanaa, in 2014.
The strike in Mukalla comes after Saudi Arabia targeted the council in air strikes on Friday that analysts described as a warning for the separatists to halt their advance and leave the governorates of Hadramout and Mahra.
The council had pushed out forces there affiliated with the Saudi-backed National Shield Forces, another group in the coalition fighting the Houthis.
Those aligned with the council have increasingly flown the flag of South Yemen, which was a separate country from 1967 to 1990.
Demonstrators have been rallying for days to support political forces calling for South Yemen to secede from Yemen.
The separatists' actions have put pressure on the relationship between Saudi Arabia and the UAE, which maintain close relations and are members of the OPEC oil cartel, but also have competed for influence and international business in recent years.
A statement from Saudi Arabia's foreign ministry directly linked the council's advance to the Emiratis for the first time.
"The kingdom notes that the steps taken by the sisterly United Arab Emirates are extremely dangerous," it said.
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