It is the first time that Seoul has pulled out all its workers from the flagship project since it was opened in 2004, underscoring the severe deterioration in relations between the two Koreas.
The Kaesong Industrial Zone -- located 10 kilometres (six miles) north of the frontier -- was once a rare symbol of cross-border cooperation, but has fallen victim to the stand-off on the Korean Peninsula.
Seoul last week ordered all remaining South Koreans to leave after Pyongyang banned entry by southerners, pulled out its own 53,000 workers and rejected the South's call for talks on the impasse.
Seoul sent two vehicles loaded with cash over the border as the last workers returned, to make the payments demanded by Pyongyang.
Tension has been high since the North, angered by fresh UN sanctions sparked by its nuclear test in February and South-US military drills, issued a series of apocalyptic threats of a nuclear war against Seoul and Washington.
Pyongyang has repeatedly blamed the South for the deadlock over the Kaesong Industrial Zone (KIZ).
"The puppet regime is getting frantic in its moves to have the KIZ closed by withdrawing all south side's personnel from it," it added.
Previously the complex had remained largely immune to strains in cross-border relations.
While neither side has gone so far as to declare a permanent shutdown, experts say the next step could be for the South to cut electricity supplies to the site.
Hong Yang-Ho, head of the Kaesong Industrial District Management Committee, expressed hope that the two sides could still secure the future of the complex.
"I believe there will be further discussion through various channels," he told reporters at the border in Paju after his return, adding that the factories were safely locked and would remain intact despite the withdrawal.
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