Johor Darul's Farizal was sent off for pushing the referee and continued using his fists to push the match official and his colleagues and brought the game into "serious disrepute", the region's governing body said in a statement.
Johor Darul, the 2015 winners, were eliminated on away goals after a 2-1 second leg win for the side from the Philippines during the match in Bacolod last week.
Johor Darul head coach Benjamin Mora Mendivil was also fined $7,000 for using insulting language at AFC staff and match officials after the game.
The AFC also suspended Jeju player Cho Yong-hyung for six months and fined the Korean $20,000 after a protest lodged by Urawa.
"Cho was expelled by the referee in the 81st minute after receiving his second caution in the match," the AFC said.
"Despite being expelled, he re-entered the field of play after the completion of the match during the post-match incident and used his hands to deliberately push the referee, an action which brings the game into serious disrepute."
His team mate Baek Dong-gyu was banned for three months and fined $15,000 for violent conduct.
"Baek, an unused substitute, was expelled by the referee for running onto the field of play in the 119th minute in an unprovoked manner and deliberately striking an opponent player's face with his elbow, an act of violent conduct," the statement added.
Baek has said he would travel to Japan to apologise for his actions.
South Korea's Yonhap News agency reported on Friday that Jeju would appeal the sanctions handed down by the AFC.
Urawa advanced to the quarter-finals of the competition after their 3-0 win in extra time gave them a 3-2 aggregate victory.
(Reporting by Sudipto Ganguly in Mumbai; editing by Peter Rutherford)
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