Three-time champion Nagoya Oceans sealed the top spot in Group D.
Mes Sungun and Oceans, who had never previously met, came into the tie having already booked their places in the knockout stage after winning both their earlier group games.
Oceans’ Tomoki Yoshikawa, Ryuta Hoshi and Pepita troubled the defending champion as the Japanese club controlled the early possession.
Alireza Vafaei and Farhad Fakhim scored for Mes Sungun.
Nagoya Oceans will face Group C runner-up Vamos FC in the quarter-finals while Mes Sungun will play Group C winner Bank of Beirut of Lebanon on Wednesday.
The 2019 AFC Futsal Club Championship is the 10th edition of the AFC Futsal Club Championship, an annual international futsal club tournament in Asia organized by the Asian Football Confederation (AFC).
The competition is being held in Bangkok, Thailand on August 7-17.