They were detained two weeks ago when Chinese police pulled them from the grounds of the Japanese consulate in the Chinese city of Shenyang.
They were allowed to leave China on Wednesday and flew to Seoul via Manila.
The five - two men, two women and a three-year-old girl, all from the same family - looked nervous but relieved.
One of the men, Kim Kwang-chul, said: "First of all, I'd like to say thanks to God and to those who helped us come here.
"We had bitter feelings because we were dragged out of the Japanese consulate compound by Chinese security authorities, but we've left all the bad feelings behind as we are now in South Korea".
The five were met by relatives who defected to South Korea last year.
They were taken to a government facility for health checks and questioning and are due later to be transferred to a special site for North Korean defectors, South Korea's Yonhap news agency reported.
Diplomatic row
Recent North Korean escapes to South via China
June 2001 Family of seven who sheltered in UN office in Beijing
March 2002 25 people who entered Spain's Beijing embassy
May 2002 Five people from US and Canadian diplomatic sites
May 2002 Five relatives taken by Chinese police from Japanese consulate
Diplomats from both sides hope the issue can now be forgotten.
The Chinese Government insisted its police had been invited into the consulate to arrest the North Koreans, while Japan said its diplomatic territory had been violated.
Japan's Prime Minister Junichiro Koizumi said the family's fate was settled because China treated the asylum seekers as unidentified people.
"If Beijing had called them North Korean nationals, the case could not have been resolved," he said, according to Kyodo news agency.
"Sometimes we have to leave something vague. That's why diplomatic negotiations are difficult."
China is North Korea's closest ally and officially regards the thousands of North Koreans who live in north east China as economic migrants who face repatriation.
But in recent cases, asylum seekers were allowed to go to South Korea, perhaps prompting other groups to try similar tactics
Wednesday's agreement to let the latest five go brings to 38 the number of North Koreans who have been allowed to leave for South Korea since early March, all of them having sought asylum in foreign diplomatic compounds.
China has become increasingly worried about the trend.
It has stepped up embassy security and compounds in Beijing are ringed with barbed-wire and surrounded by armed guards, some even wielding baseball bats.