Government troops also retook the international airport in Aden, a main hub for the southern part of the country, Yemen's information minister said. Many predicted the city would soon fall back into government hands.
The rapid advance by government forces underscored the seesaw nature of the fighting. Only weeks before, the separatists had gained much territory in southern Yemen, pushing government forces out of strategic cities and areas.
The fighting between the two sides has added another layer to the complex civil war in the Arab world's most impoverished country, a war pitting a Saudi-led coalition backing the government against the Houthi rebels who control the country's north. The separatists and the government are ostensibly allies in that fight.
Earlier in the day, government forces pushed the UAE-backed separatist militia known as the Security Belt out of the city of Zinjibar, the capital of southern Abyan province, following clashes that left at least one fighter dead and 30 wounded. The separatists had seized Zinjibar earlier this month.
Retreating from Zinjibar, the separatists fled to nearby Aden province, which they had taken from forces of Saudi-backed President Abed Rabbo Mansour Hadi earlier this month, the officials said.
Government forces then continued their push to retake the city of Aden, which has functioned as the seat of Hadi's government since the Iran-backed Houthi rebels captured Sanaa, Yemen's capital, and much of the north in 2014.
Hadi's forces first reclaimed the eastern district of Khor Maksar, and then moved to the neighborhood of Crater in Aden, where the presidential palace is located, the officials said.
Saudi Arabia and Emirati forces have guarded the palace since the separatists pushed the presidential guards out of the city.
Information Minister Moammar al-Iryani said government forces reclaimed Aden's airport. "National army forces entered Aden airport and have taken full control of the main gate of the airport amid public celebration and joy," he tweeted.
"The return of the state to Aden is a victory for the people," said Maeen Abdulmalik Saeed, Yemen's prime minister.
Hadi's supporters were seen in videos posted online dancing in the streets of Zinjibar and Aden, and welcoming government forces. Videos show Hadi's fighters on the streets of Khor Maksar carrying machine guns and cheering.
Local residents said the UAE-backed separatists fled to nearby Lahij and Dhale provinces.
Security officials said the separatists still controlled Jabal al-Hadid military camp, one of the main military facilities Aden. The Security Belt militia were also still in their camps in Aden.
Saudi officers were working with both sides to avoid fighting in the densely populated areas and convince them to attend the reconciliation talks in Saudi Arabia, the officials said.
But later, security officials said the Saudi-led coalition carried out an airstrike close to a military camp in Aden's Dar Saad district. Witnesses said a bus in the area was hit, killing an unknown number of civilians.
Another airstrike hit an unidentified target in eastern Aden, the officials said. They said the coalition has warned both sides that it will strike either side moving on the ground.
The officials spoke on condition of anonymity because they were not authorized to brief the media, and the witnesses demanded anonymity for fear of reprisal.
In a 48-second audio message, Aidarous al-Zubaidi, a former Aden governor who leads the separatist Southern Transitional Council, called on his forces to resist. He said the separatists have fought a "battle of fate against terrorism and extremism."
His deputy Hani Bin Braik, a former Cabinet minister, also tweeted Wednesday that "Aden is OK." He said separatist forces "are pouring in for the great battle of dignity."
Residents in Aden said militiamen on dozens of vehicles arrived in the city late Wednesday from nearby Dhale province to support the Southern Transitional Council. The residents reported fighting between government forces and separatists in Al-Maala district.
The latest push by Hadi's government comes days after the Saudi-led coalition called for a cease-fire and invited both sides to reconciliation talks in Saudi Arabia. The coalition also urged the separatists to withdraw from all government buildings and military bases.
The government said it would not engage in talks before the separatists pulled out, while government supporters demanded the UAE withdraw from the Saudi-led coalition. The calls prompted Saudi Arabia and the UAE to issue a joint statement, pledging to keep up their floundering coalition and focus on the war against the Houthis.
The fighting between Hadi's forces and the UAE-backed militias erupted earlier this month amid urgings by the separatist Southern Transitional Council for the militias to "topple" Hadi's government. The UAE is a key member of a Saudi-led coalition that has been battling the Houthis since March 2015 on behalf of Hadi's government.
But despite having a common enemy, relations between the two sides have been tense amid allegations the Emiratis have offered patronage to southern Yemeni politicians campaigning for secession, as well as what Hadi perceives as UAE violations of his country's sovereignty. Yemen was split into two countries during much of the Cold War before unifying in 1990.
The fighting came weeks after the UAE pulled an unspecified number of troops from Yemen. Yemeni officials have suggested Emirati troop strength dropped by as much as 75%.
The Emirati withdrawal followed rising tensions between Iran and the U.S. over Tehran's collapsing nuclear deal with world powers, suggesting Abu Dhabi worried about having forces away from home if an armed conflict broke out.
Meanwhile, Saudi Arabia said early Thursday that a Houthi strike hit Abha regional airport, causing no injuries. The Houthis said they attacked the facility with a Quds-1 cruise missile late Wednesday. Attacks targeting that airport over recent weeks have wounded dozens and killed at least one person.