The Norwich City forward is accused of filming a sexual encounter with the former partner on his phone without consent. He denies the allegation.
Hwang played for South Korea in two World Cup qualifiers this month, scoring a penalty against Singapore, but the Korea Football Association (KFA) on Tuesday suspended him pending the outcome of police investigations.
The 31-year-old remains able to play for English second-tier club Norwich and scored in a 3-2 defeat at Watford on Tuesday.
"Until a definitive conclusion is drawn, we have decided to exclude Hwang from the national team," a KFA statement said.
Lee Youn-nam, who heads the KFA's ethics committee, told reporters that national players must conduct themselves "with a high degree of morality and responsibility."
"Considering the fact that the player is being investigated as a suspect, it is difficult for him to carry out normal national team activities," Lee said.
"Football fans have high expectations for the national team, (so) we have deemed it inappropriate to select Hwang Ui-jo for the national team."
Hwang, who is on loan at Norwich from Nottingham Forest, has scored 19 goals in 62 appearances for South Korea.
Coach Jurgen Klinsmann said in a statement issued by the KFA: "I fully understand the current situation and will respect the decision of the Korea Football Association."
Klinsmann picked Hwang for recent World Cup qualifying wins over Singapore and China, after the police had begun their probe, and defended his decision at the time.
"There is always speculation," said the German World Cup winner after returning from the 3-0 win over China in Shenzhen last week.
"Until there's nothing proven... I don't believe it."
The Asian Cup kicks off in Qatar on Jan. 12, with South Korea opening their campaign against Bahrain three days later.