The banner, which read "Annihilate British Dogs, Eradicate Hong Kong Independence Poison", was displayed late in Guangzhou's 6-0 win over the Hong Kong champions.
Guangzhou, two-time winners of the continental club competition, have been charged with two offences, the first under Article 58 of the AFC's disciplinary and ethics code and the second under Article 65, which relates to spectator misconduct.
Japan's Kawasaki Frontale have also been charged by the AFC under Article 58 after fans of the club displayed a wartime flag at their meeting with South Korea's Suwon Bluewings at Suwon World Cup Stadium.
Officials travelling with the club reportedly confiscated the flag, used by the Imperial Japanese Army until the end of World War II, from two men while other supporters were escorted from the stadium.
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Lebanon's Nejmeh also face being sanctioned under articles 58 and 65 for incidents during their meeting with Jordan's Al Wehdat in the AFC Cup last week.
(Reporting by Michael Church, Editing by Sudipto Ganguly)
