Witnesses told Xinhua that security forces loyal to the STC also surrounded and stormed the 4th Presidential Guard camp in the eastern part of Aden.
But tension between the allies began to surface in April when Hadi dismissed cabinet minister Hani bin Breik and Aden s governor in a move widely seen as reflecting divisions among his supporters.
In a post on Twitter, Mukhtar al-Rahbi, an official in Yemen's government, said: "A plane from the Arab coalition, that said it had come to support legitimacy (Yemen's internationally recognised government) bombed the base of the Fourth Brigade".
Hani bin Bourek, a senior member of the Southern Transitional Council, said the separatists had pulled their forces back after mediation by other members of the Saudi-led coalition.
According to Yemen's official SABA news agency, President Abdrabbuh Mansur Hadi convened an emergency meeting to discuss what he described as "an illegitimate coup attempt by the so-called Southern Transitional Council (STC)".
The International Committee of the Red Cross (ICRC) placed the casualty count to at least 36 killed and 185 injured.
The U.N. Office for the Coordination of Humanitarian Affairs said in a statement that the situation has "restricted staff movements in and outside of Aden" and that humanitarian flights are on hold after the closure of the airport.
The Saudi-led coalition, which intervened in Yemen's civil war in 2015 to restore President Abed Rabbo Mansour Hadi's government from the Iran-backed Houthis, called on both parties to cease hostilities.
On Sunday, security sources said pro-separatist units trained and backed by the United Arab Emirates had taken over the government headquarters in Aden after clashes.
The coalition also imposed air and sea blockade to prevent weapons from reaching Houthis, who are in control of most of the northern Yemeni provinces, including the capital Sanna.
In the past months, government forces and the UAE armed forces operating in Aden province launched an anti-terror offensive to root out Al Qaeda militants from their strongholds in the neighbouring province of Abyan.