The court found Hwang, 56, had embezzled the funds for a fake stem cell experiment and breached bioethics laws in purchasing human eggs, Yonhap news agency reported.
The court imposed a two-year sentence suspended for three years. The prosecution had asked for a four year jail term.
"The nature of Hwang's crimes is grave, given that he violated laws to use human eggs and misappropriated a combined 830 million won ($704,000) by issuing fake tax bills and did not return the money," the court said.
Hwang, a former veterinary professor at Seoul National University, gained fame for claiming success in cloning human embryonic stem cells. He was charged in 2006 with misappropriating research funds and illegally purchasing human eggs.