Seven of the aid workers were handed over to the International Committee of the Red Cross in two groups in the central province of Ghazni where they were captured July 19.
A dozen others were freed on Wednesday, a day after South Korean negotiators struck a deal with Taliban negotiators.
The freed hostages were "very, very happy and look healthy," ICRC official Irfan Sulejmani said just minutes after the last three South Koreans were picked up in a remote field in the central province of Ghazni in the dark of night.
They were driven to Ghazni town, about 30 minutes away, where they and the others were handed over to a South Korean delegation in the offices of the Red Crescent Society, Mr Sulejmani said.
The Red Crescent compound was the venue of crucial talks between Taliban and a South Korean delegation to free the Christians aid workers seized while travelling on a major highway through the risky area by bus.
The Taliban captured 23 and killed two of them days later as the government rejected their demand for militant prisoners to be freed from jail.
The extremists then released two on August 13 as a "gesture of goodwill" to talks with the South Koreans.
The release of the final seven was like a light at the end of a "very dark tunnel," a South Korean diplomat in Kabul said.
The aid workers would leave Afghanistan as soon as possible, he said on condition of anonymity. "It could take one or two days," he said.
The official would not say where the 12 freed Wednesday had spent the night but said they were in a "safe place."
Relief and criticism
In Seoul there was relief as the ordeal drew to a close, but also some criticism.
The father of one of the killed missionaries slammed the church behind their ill-fated trip.
"I wonder why the church was so reckless in taking them to the dangerous country," said Shim Chin-Pyo, whose 29-year-old son was killed.
"They were in the wrong place at the wrong time, moving in such a conspicuous manner."
The Taliban militia said it had agreed to free its 19 remaining hostages following South Korea's promise to withdraw its military force from Afghanistan, as planned, and ban missionary groups from the country.
The deal has raised questions in Seoul about the diplomatic damage that could be caused by negotiating directly with the hardline Islamic militia.
Afghan Foreign Minister Rangeen Dadfar Spanta told Germany's RBB-Inforadio that it sent "a very dangerous message to the world" when governments were seen as giving into "blackmail."
The saga could be seen as a victory for the Taliban, he said.
"It was a blow to the government and a positive point for the Taliban," an official said in Kabul on condition of anonymity.
Canadian Foreign Minister Maxime Bernier was also critical of negotiations with "terrorists."
"Such negotiations, even if unsuccessful, only lead to further acts of terrorism," the minister said in a statement.