"As a result of comments ... the AFC has opened disciplinary proceedings based on Article 50.1 of the AFC Disciplinary and Ethics Code (Bringing the game into disrepute)," the confederation said in a statement.
"The case will be dealt with by the AFC Disciplinary and Ethics Committee on a date to be confirmed."
Villas-Boas blasted the AFC and match officials overseeing both legs of the Asian Champions League quarter-final, claiming twice former champions Guangzhou were receiving preferential treatment.
"In the last game Fu Huan had a very clean slide tackle which led to his suspension in this match," said the former Chelsea and Porto boss.
"Yan Junling is suspended for the first leg of the semi-final because the referee gave him a yellow card. The referee chose the end of the Guangzhou fans to take the penalties. The referee gives two red cards to our players.
"Zhang Linpeng should be suspended from this game because he used his elbow in the first game and he's not suspended because the committee of ethics and discipline at AFC did not judge an elbow as violent conduct."
The coach also accused Guangzhou of engineering car accidents as the SIPG team bus made its way to the ground.
"This is the greatest achievement for SIPG ever because it's against a club that is dominating the AFC," the former Chelsea and Tottenham Hotspur manager said.
"This club can do everything, they can cause accidents in front of us, they have players who can elbow Elkeson and not be suspended and yet we won. The referee gave our goalkeeper a yellow card during the penalties and this is a disgrace.
"It's a disgrace."
Villas-Boas has already fallen foul of the authorities this season having been handed a two-game ban in the Chinese Super League for questioning an eight-game suspension handed to SIPG's Oscar.
SIPG will meet Japan's Urawa Red Diamonds in the semi-finals, with the first leg to be played on September 27 and the return three weeks later.
(Reporting by Michael Church, Editing by Amlan Chakraborty)
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