Afghan authorities recovered his blood-stained body dumped southwest of Kabul.
South Korea's foreign ministry confirmed the body was that of Shim, one of 23 Korean Christians, 18 of them women, taken captive by the Taliban nearly two weeks ago.
The bullet-ridden body of the first victim Bae Hyung-kyu, a male pastor who led the group, was found last Wednesday.
Shim's mother cried hysterically when she arrived at the Saemmul Church in suburban Seoul after hearing the victim may have been her son.
"Why did you kill him? Please save his life," Shim's mother said through her tears.
Shim's father, a provincial assembly member, described his son as a gentle soul.
"He had a good heart and did a lot of volunteer work. My son also wanted to help the poor and disabled," Shim Chin-pyo told reporters.
Shim was unemployed and looking to go to graduate school, local media reported. One aunt said relatives were trying to set him up to get married next year, Yonhap news agency reported.
Analysts said there was no easy answer for the South Korean government, which sent a special envoy to Afghanistan, to resolve the problem. Seoul has few people with expertise in the region and almost no experience in negotiating with the Taliban.
South Korea had strongly advised groups not to go to Afghanistan due to safety concerns.
On Monday, the body of the first victim Bae, 42, who left behind a wife and 9-year-old daughter, arrived in South Korea.
His brother, Bae Shin-kyu, told reporters the family would not have a funeral until the other hostages were returned to South Korea.
