South Korean parliament, the National Assembly, endorsed the appointment of Hwang, 58, in a 156-120 vote, Yonhap news agency reported.
Former prime minister Lee Wan-koo had stepped down in late May amid bribery allegations.
The appointment follows calls from the government and the ruling party for speedy parliamentary approval of a prime minister, who would take charge in the government efforts against the rapid spread of the MERS virus.
Since the outbreak of the first case here May 20, the acute respiratory virus has killed 23 South Koreans as of Thursday. The total number of MERS cases have risen to 165.