Wednesday brought the conclusion of an airlift of about 12,000 South Sudanese, organizers said. Yet hundreds of thousands of ethnic southerners are thought to still be living in Sudan.
South Sudan seceded from Sudan in July under a 2005 peace deal, but the two sides are still at odds over issues including the position of the shared border, oil revenues and the status of citizens in one another's countries.
Fierce border clashes between the two sides in April threatened to spark an all-out war and scuppered the signing of a deal that would have helped resolve the status of southerners in Sudan.
Khartoum said it would begin to treat South Sudanese as foreigners after a deadline expired in April to get residency papers or leave.
The International Organization for Migration (IOM) arranged dozens of flights for southerners who had been ordered to leave the way station of Kosti, where they were stranded on their way to South Sudan.
The last flight left on Wednesday afternoon from Khartoum airport.
"I hope that my brothers and sisters who are still here return," Martin Simon, a southerner boarding the flight, said.
Southerners still in Sudan
Jill Helke, IOM's chief of mission in Sudan, said hundreds of thousands of southerners were still believed to be in Sudan, but the organization did not have the funding to move them all.
"At the moment the [Nile] barges are not allowed to move, the roads are not safe and the trains are not functioning," she told Reuters at the airport. "We hope if peace negotiations go well that all these avenues for land transportation will open up."
It is unclear exactly how many southerners are still in Sudan, but estimates have ranged from around 350,000 to as many as 700,000.
Some 2 million people died in Sudan's civil war, fought for most years between 1955 and 2005 over ideology, religion, oil and ethnicity.