The South Korean hosts were controversially awarded two late penalties by Qatari referee Fahad Jaber Al Marri, with Rafael Costa converting the second deep into stoppage time to salvage a point.
Hiroki Mizumoto received his marching orders for a second bookable offence in the incident that led to the first spot-kick, which was blocked by goalkeeper Takuto Hayashi, before Kazuhiko Chiba was penalised for what appeared to be an equally innocuous incident five minutes later.
Victory for Sanfrecce would have seen them move top of the group and three points clear of basement side FC Seoul, and the Japanese club have now opted to make their feelings known to the governing body.
"We, Sanfrecce Hiroshima, have submitted a letter of appeal to the AFC today (Wednesday) regarding the referees’ judgments at yesterday's match - AFC Champions League group stage round 4 vs FC Seoul at Seoul World Cup Stadium - that there are possibly some intentional judgments that affected the result through the whole game," a club statement read.
"We cannot accept those refereeing standards at the tournament to determine the Asian Champion.
"We, Sanfrecce Hiroshima sincerely hope to improve the refereeing and will continue to deal with this issue with JFA and J-League."
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