The move came as Middle Eastern and Western diplomats gathered in Jordan for high-level talks on Syria, and a day after nationwide celebrations at Assad's ouster.
Ankara has been a major player in Syria's conflict, holding considerable sway in the northwest and financing armed groups there, and maintaining a working relationship with the Islamist Hayat Tahrir al-Sham (HTS), which spearheaded the offensive that brought down Assad.
Turkey's Foreign Minister Hakan Fidan said the new charge d'affaires, Burhan Koroglu, left for Syria on Friday, with the embassy expected to be "operational" the following day.
Fidan also said Ankara had urged Assad backers Russia and Iran not to intervene as the Islamist-led rebels mounted their lightning advance last week.
"The most important thing was to talk to the Russians and Iranians to ensure that they didn't enter the equation militarily... They understood," Fidan told private television network NTV.
Turkish diplomats joined counterparts from the European Union, the United States and the Arab world on Saturday for talks in the Jordanian city of Aqaba.
UN special envoy for Syria Geir Pedersen urged participants to provide humanitarian aid and to ensure "that state institutions do not collapse".
"If we can achieve that, perhaps there is a new opportunity for the Syrian people," he said.
US Secretary of State Antony Blinken, on a regional Syria-focused tour, also joined the Aqaba meeting.
A Qatari diplomat, meanwhile, said a delegation from the Gulf emirate would visit Syria on Sunday to meet transitional government officials on aid and the reopening of its embassy.
Unlike other Arab states, Qatar never restored diplomatic ties with Assad after a rupture in 2011.
Assad has fled Syria, closing an era in which suspected dissidents were jailed or killed, and capping nearly 14 years of war that killed more than 500,000 people and displaced millions.
'Tears of joy'
A day before the meetings in Jordan, Syrians had celebrated what they called the "Friday of victory", with fireworks heralding the fall of the Assad dynasty.
Celebrations continued into the night on the first Friday -- the Muslim day of rest and prayer -- since Assad was ousted.
Umayyad Square in Damascus was jammed with vehicles, people and waving flags as fireworks shot into the air, AFPTV footage showed.
Crowds also gathered in the squares and streets of other Syrian cities, including Homs, Hama and Idlib.
Ahmad Abd al-Majed, 39, an engineer who returned to Aleppo from Turkey, said that many shed "tears of joy and happiness".
"Syrians deserve to be happy," he said.
In the southern city of Sweida, the heartland of Syria's Druze minority, Bayan al-Hinnawi, 77, never believed he would live to see such a day.
"It's a wonderful sight. Nobody could have imagined this could happen", said Hinnawi, who spent 17 years in prison.
Sunni Muslim HTS is rooted in Syria's branch of Al-Qaeda and is designated a "terrorist" organisation by many Western governments.
But the group has sought to moderate its rhetoric, and the interim government insists the rights of all Syrians will be protected, as will the rule of law.
The European Union was seeking "to establish contacts" with the new rulers soon, an EU official told AFP on condition of anonymity.
Inside much of the country, the focus turned towards unravelling the secrets of Assad's rule, particularly the network of detention centres and suspected torture sites.
The International Committee of the Red Cross said it documented more than 35,000 disappearances during Assad's rule, with the actual number likely far higher.
"We just want a hint of where they were," Abu Mohammed told AFP as he searched for news of three missing relatives at the Mazzeh airbase in Damascus.
While Syrians celebrate the end of Assad's brutal rule, they face a struggle for necessities in a country ravaged by war, sanctions and runaway inflation.
On Friday, the EU announced the launch of an "air bridge" operation to deliver an initial 50 tonnes of health supplies via neighbouring Turkey.
Israeli strikes
Assad was propped up by Russia -- where a senior Russian official told US media he has fled -- as well as Iran and Lebanon's Hezbollah militant group.
The rebels launched their offensive on November 27, the same day a ceasefire took effect in the Israel-Hezbollah war in Lebanon, in which Assad's ally suffered staggering losses.
Both Israel and Turkey have carried out strikes inside Syria since Assad's fall.
A Syria war monitor said Israeli strikes early Saturday "destroyed a scientific institute" and other related military facilities in Barzeh, in northern Damascus, and targeted a "military airport" in the capital's countryside.
Strikes also hit targets in the Qalamun area, the Syrian Observatory for Human Rights added.
The Observatory said several rounds of bombardment targeted "military sites of the former regime forces, as part of destroying what is left of the future Syrian army's capabilities".
The army has been ordered to "prepare to remain" there throughout the winter, Defence Minister Israel Katz's office said Friday.
