The transfers came as Russian-backed government forces advanced in the neighbouring province of Quneitra, with air strikes pounding rebel positions perilously close to the Israeli-occupied Golan Heights.
After securing Damascus in May, President Bashar al-Assad turned his attention to rebels in the strategically vital south, where protests against his rule first erupted seven years ago.
Nearly three weeks of bombardment saw beleaguered rebels agree with Russia earlier this month to hand over Daraa province, before reaching a similar deal for its capital this week.
In recent days, rebels have handed heavy-duty arms and equipment to government forces who entered the city's rebel-held southern districts for the first time in years and raised the national flag.
On Sunday, rebels and civilians who did not want to live under regime control were granted safe passage to opposition-held Idlib in Syria's northwest.
Hundreds of fighters and some relatives, carrying suitcases packed with clothes, boarded around 15 buses in Daraa city, AFP's correspondent there said.
The vehicles, parked on a main thoroughfare connecting the city's government-held north with its rebel south, were searched by Russian forces before setting off just after midday for Idlib.
"My heart is aching and in pieces. May God recompense us. What more can I say?" said Huzayfa Halawa, a 28-year-old rebel evacuated on Sunday.
Buses leave, buses stay
The official news agency SANA said on Sunday Daraa's rebels released five men they had been holding hostage into regime custody, and also surrendered more heavy and medium weaponry.
That would pave the way for the entire city to come under government control in accordance with the handover deal.
A small group of Syrian soldiers took up position in Daraa al-Balad on Sunday, a key rebel-held quarter, said the Syrian Observatory for Human Rights monitor.
It said 430 people including civilians and rebels from the city and wider province were evacuated, far fewer than the 1,400 expected to leave.
"There are still empty buses in the city and it is unclear if there will be more evacuations," said the head of the Britain-based group, Rami Abdel Rahman.
The deal for Daraa city is the latest in a string of such agreements the regime has used to retake large parts of the country.
They usually follow ferocious military campaigns and sometimes stifling sieges that effectively force rebels to surrender.
Their terms also typically include the mass transfer of thousands of rebels and civilians to opposition-held Idlib, in what rights groups and activists say may amount to forced displacement.
Moscow has brokered many of these deals. It had reportedly insisted to southern rebels such transfers were not on the table for them, but seems to have ultimately relented.
Top Iran official in Syria
The regime fully regaining Daraa will be a significant blow to the opposition.
In 2011, teenagers were arrested for scrawling anti-Assad slogans on a school in the city, sparking mass protests against the government.
A brutal crackdown paved the way for a full-fledged conflict that has since killed more than 350,000 people and displaced millions.
Assad has regained much of the territory he lost to rebels, now comfortably controls more than 60 percent of Syria.
In the south, he holds 80 percent of Daraa province but parts of its western countryside and most of the adjacent province of Quneitra still escape his control.
On Sunday, regime forces battered Quneitra province with hundreds of missiles and seized the town of Masshara, according to the Observatory.
The clashes killed 20 regime forces and 17 rebels, the monitor said.
Air strikes also hit an opposition position in Quneitra that lies within four kilometres (less than three miles) from the sensitive buffer zone with the Israeli-annexed Golan Heights.
The Observatory said the suspected Russian strikes were the first in the area in over a year, when Moscow, Washington, and Amman agreed a ceasefire for parts of the south.
Around 160,000 people who were displaced by the regime's offensive on Daraa are still trapped in Quneitra, near the border with the Golan.
Israel has been on high alert in recent weeks amid the spike in hostilities in the south.
It says its main priority is preventing its archfoe Iran, a key backer of Assad, from building up its military installations in Syria.
On Sunday, Hossein Jaberi Ansari, a senior aide in Iran's foreign ministry, met with Assad in Damascus and hailed Syria's advances in Daraa, according to the Syrian presidency.