The workers had stayed behind after the other South Korean staff had left to negotiate wages demanded by North Korea.
Kaesong Industrial Complex has been at a standstill since North Korea withdrew its 50,000 workers in April.
North Korea has previously restricted entry to Kaesong joint industrial zone, but this is the first time all South Koreans have withdrawn.
Kaesong Industrial Complex, which was launched in 2003, was seen as one of the last remaining symbols of inter-Korean co-operation.
North-South tensions escalated following Pyongyang’s third nuclear test in February.
The last seven South Korean workers had been expected to cross the border at 17:30 local time on Friday.
“The return was delayed a little [today] due to some technical procedure issue,” said Hong Yang-Ho, head of the Kaesong Industrial District Management Committee
“The North [Korea] fully co-operated during our returning process.”
Hong Yang-ho also said he believes there will be discussions about the future of the complex, but did not elaborate further.
South Korean vehicles loaded with outstanding North Korean wages and taxes worth $13 million crossed into the North at the same time the workers returned.
Those delivering the money have also returned to South Korea, reports say.
The zone is home to 123 South Korean companies which employ North Korean workers, and provides the North with badly-needed hard currency.
North Korea blocked South Korean workers from entering the zone in April, and withdrew its 53,000 workers from the industrial park a few days later.
After North Korea rejected Seoul’s calls for talks on resuming operations at the park, South Korea announced that it too would withdraw all its workers from the complex.
It pulled out 125 South Koreans last week and another 43 on Monday, leaving the final seven to “settle accounting and other unresolved matters”.
Pyongyang has been angered by tightened UN sanctions imposed after its February 12 nuclear test and by joint US-South Korea military drills, which it has described as “attack rehearsals”.
On Thursday, North Korea sentenced a US citizen to 15 years of hard labor for alleged anti-government crimes.
American citizen Pae Jun-ho, known in the US as Kenneth Bae, was detained last year after entering North Korea as a tourist. Analysts suggest Pyongyang could be using the jailed American as leverage.
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