Taliban and Afghan officials have also denied that a ransom was involved.
But Alan Fisher, reporting for Al Jazeera from Kabul in Afghanistan, said that the "Taliban left the table substantially richer" and that the ransom could have been as high as $20m.
"We've gone back to several sources and again they have told us that as far as they are aware there was certainly a ransom paid and a figure that is being bandied around in Kabul is about $20m ... All our sources tell us that money did change hands."
He also reported that kidnappings by the Taliban were likely to continue.
"In a vow to continue with the kidnappings they [the Taliban] said that 'we will do the same thing with other allies in Afghanistan because we found this way to be successful'," he said.
Seoul had earlier restated its decision to withdraw its small military presence in Afghanistan - about 200 people comprised mainly of medical workers and engineers - by the end of the year.
It also agreed with the Taliban that it would ban missionary groups from going to Afghanistan, prompting criticism from the Korea World Missions Association.
"Korean churches cannot help expressing deep concerns over the agreement reached between the government and the Taliban to halt missionary activities in Afghanistan," the organistaion said in a statement.
The Taliban originally kidnapped 23 South Korean hostages on July 19, later killing two of them.
Shim Jin-Pyo, the father of one of the hostages who was killed by the Taliban, asked: "How could the Taliban kill him and throw his body on the street like a dog?"
"He was only trying to help children who had suffered in the war," he told Al Jazeera.
In mid-August, the Taliban freed two women, as direct talks with Seoul got under way following the failure of negotiations with Afghan mediators.
Kabul refused a demand to free Taliban prisoners in exchange for the group.
They freed two women in mid-August as direct talks with Seoul got under way, following the failure of negotiations with Afghan mediators as Kabul rejected a demand to free Taliban prisoners in exchange for the group.
The Taliban later freed the 19 remaining Christian aid workers over Wednesday and Thursday.
Critics have also hit out at the Afghan government, saying that the deal with the Taliban was a propaganda victory for the religious group.
Rangeen Dadfar Spanta, the Afghan foreign minister, said on Germany's RBB radio that "if the impression is created now that the international community and the Afghan government allow themselves to be blackmailed, then this sends a very dangerous message".
German politicians also criticised South Korea's handling of the crisis, Angela Merkel, the German chancellor, saying Berlin would stand firm in its refusal to negotiate over a German engineer captured by the Taliban more than six weeks ago.
Though the Taliban appeared to win only minor concessions from the South Koreans, some analysts have said the group has gained status from the negotiations.
But Homayun Hamidzada a spokesman for the Afghan authorities, said: "There is no victory for the Taliban. It shows the true face of the terrorists, of the Taliban."
He said Kabul had not dealt with the group. "We are glad they [the South Koreans] are out", he said, but insisted: "the Afghan government did not negotiate with the Taliban".
Prior to the kidnapping, South Korea had warned its citizens not to travel to Afghanistan and blocked many of its growing numbers of evangelical Christians from going there due to safety concerns.